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ORCIDJournal of Chemical Information and Modeling, Volume 64
Volume 64, Number 1, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Kenneth M. Merz Jr.
:
In Memoriam: Dr. George W. A. Milne. 1-2 - Andrew Rusinko III, Mohammad A. Rezaei, Lukas Friedrich, Hans-Peter Buchstaller, Daniel Kuhn, Ashwini Ghogare:
AIDDISON: Empowering Drug Discovery with AI/ML and CADD Tools in a Secure, Web-Based SaaS Platform. 3-8 - Esther Heid, Kevin P. Greenman, Yunsie Chung, Shih-Cheng Li, David E. Graff, Florence H. Vermeire, Haoyang Wu, William H. Green Jr., Charles McGill:
Chemprop: A Machine Learning Package for Chemical Property Prediction. 9-17 - Oleg Mikhailovskii, Sergei A. Izmailov, Yi Xue, David A. Case, Nikolai R. Skrynnikov:
X-ray Crystallography Module in MD Simulation Program Amber 2023. Refining the Models of Protein Crystals. 18-25 - Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, Marc Baaden, Patrick Fuchs, Tatiana Galochkina, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora, Antoine Taly:
A Perspective on the Prospective Use of AI in Protein Structure Prediction. 26-41 - Varvara Voinarovska, Mikhail Kabeshov, Dmytro Dudenko, Samuel Genheden, Igor V. Tetko:
When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. 42-56 - Zhuohang Yu, Zengrui Wu, Ze Wang, Yimeng Wang, Moran Zhou, Weihua Li, Guixia Liu, Yun Tang:
Network-Based Methods and Their Applications in Drug Discovery. 57-75 - Chunxiang Peng, Fang Liang, Yuhao Xia, Kai-Long Zhao, Minghua Hou, Gui-Jun Zhang:
Recent Advances and Challenges in Protein Structure Prediction. 76-95 - Ning-Ning Wang, Bei Zhu, Xin-Liang Li, Shao Liu, Jian-Yu Shi, Dong-Sheng Cao:
Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities. 96-109 - Ruihan Zhang, Xingran Xie, Dongxuan Ni, Hairong Wang, Jin Li, Weilie Xiao:
MT-EpiPred: Multitask Learning for Prediction of Small-Molecule Epigenetic Modulators. 110-118 - Yuto Matsumoto, Hiroaki Gotoh:
Compound Classification and Consideration of Correlation with Chemical Descriptors from Articles on Antioxidant Capacity Using Natural Language Processing. 119-127 - Arnab Bose, Gabriel A. Valdivia-Berroeta, Nina C. Gonnella:
Predicting Autoxidation of Sulfides in Drug-like Molecules Using Quantum Mechanical/Density Functional Theory Methods. 128-137 - Jiwon Seo, Ravi Singh, Jonghyuk Ryu, Jun-Ho Choi:
Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions. 138-149 - Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H. Sauer, Magnus Wolf-Watz:
Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. 150-163 - Alejandro Rivera-Pousa, Raúl Lois-Cuns, Martín Otero-Lema, Hadrián Montes-Campos, Trinidad Méndez-Morales, Luis M. Varela:
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids. 164-177 - Gaurav Jhaa, Pattath D. Pancharatna, Musiri M. Balakrishnarajan:
Alternatives for Epoxides in Graphene Oxide. 178-188 - Aitor Valdivia, F. Javier Luque, Salomé Llabrés:
Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations. 189-204 - Jacqueline C. Calderón, Eva Plut, Max Keller, Chiara Cabrele, Oliver Reiser, Francesco L. Gervasio, Timothy Clark:
Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. 205-218 - Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey:
Redocking the PDB. 219-237 - Zhong-Hao Ren, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Zheng-Wei Li, Shanwen Zhang, Xiangxiang Zeng, Yi-Fan Shang:
SiSGC: A Drug Repositioning Prediction Model Based on Heterogeneous Simplifying Graph Convolution. 238-249 - Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio:
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. 250-264 - Toby E. King, James R. Humphrey, Charles A. Laughton, Neil R. Thomas, Jonathan D. Hirst:
Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. 265-275 - Afshin Zamani Zakaria, Alpeshkumar K. Malde, Tim Gould:
Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers. 276-288 - Bing Rao, Xuan Yu, Jie Bai, Jun Hu:
E2EATP: Fast and High-Accuracy Protein-ATP Binding Residue Prediction via Protein Language Model Embedding. 289-300 - Jiaxuan Li, Lei Wang, Zefeng Zhu, Chen Song:
Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. 301-315 - Haoqing Yu, Ruheng Wang, Jianbo Qiao, Leyi Wei:
Multi-CGAN: Deep Generative Model-Based Multiproperty Antimicrobial Peptide Design. 316-326
Volume 64, Number 2, January 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Jawad Chowdhury, Charles Fricke, Olajide Bamidele, Mubarak Bello, Wenqiang Yang, Andreas Heyden, Gabriel Terejanu:
Invariant Molecular Representations for Heterogeneous Catalysis. 327-339 - Gen Li, Sijie Yao, Long Fan:
ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks. 340-347 - Ya Chen, Thomas Seidel, Roxane Axel Jacob, Steffen Hirte, Angelica Mazzolari, Alessandro Pedretti, Giulio Vistoli, Thierry Langer, Filip Miljkovic, Johannes Kirchmair:
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation. 348-358 - Yu Yin, Zhen Yang, Na Li, Xuan Yu, Mei-ling Chen, Meng Wang, Xiao-liang Ren:
Least Absolute Shrinkage and Selection Operator-Based Prediction of the Binding Constant of p-Sulfonatocalix[6]/[8]arenes with Alkaloids. 359-377 - Julian M. Delgado, Péter R. Nagy, Sameer Varma:
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes. 378-392 - Mateus Sá Magalhães Serafim, Thales Kronenberger, Rafael Eduardo Oliveira Rocha, Amanda Del Rio Abreu Rosa, Thaysa Lara Gonçalves Mello, Antti Poso, Rafaela Salgado Ferreira, Jonatas Santos Abrahão, Erna Geessien Kroon, Bruno Eduardo Fernandes Mota, Vinicius Gonçalves Maltarollo:
Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. 393-411 - Marco Foscato, Giovanni Occhipinti, Sondre H. Eliasson, Vidar R. Jensen:
Automated de Novo Design of Olefin Metathesis Catalysts: Computational and Experimental Analysis of a Simple Thermodynamic Design Criterion. 412-424 - Matthew S. Smith, Ian S. Knight, Rian C. Kormos, Joseph G. Pepe, Peter Kunach, Marc I. Diamond, Sarah H. Shahmoradian, John J. Irwin, William F. Degrado, Brian K. Shoichet:
Docking for Molecules That Bind in a Symmetric Stack with SymDOCK. 425-434 - William T. Higgins, Sandip Vibhute, Chad Bennett, Steffen Lindert:
Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. 435-448 - Midhun K. Madhu, Kunal Shewani, Rajesh K. Murarka:
Biased Signaling in Mutated Variants of β2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. 449-469 - Amanda C. Macke, Jacob E. Stump, Maria S. Kelly, Jamie Rowley, Vageesha Herath, Sarah Mullen, Ruxandra I. Dima:
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-Based Algorithms. 470-482 - Deepak Ahire, Charles Mariasoosai, Siavosh Naji-Talakar, Senthil Natesan, Bhagwat Prasad:
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches. 483-498 - Maya Petgrave, Shubham Devesh Ramgoolam, Aravindhan Ganesan:
Deciphering the Molecular Association of Human CRIP1a with an Agonist-Bound Cannabinoid Receptor 1. 499-517 - Charlotte Bouquiaux, Benoît Champagne, Pierre Beaujean:
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes. 518-531 - Yusuke Miyazaki, Wataru Shinoda:
pSPICA Force Field Extended for Proteins and Peptides. 532-542 - Santiago Antolínez, Peter Eugene Jones, James C. Phillips, Jodi A. Hadden-Perilla:
AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. 543-554 - Juan I. Felice, Verónica Milesi, Gabriel Fabricius:
Exploration of the Parameter Space of an Ion Channel Kinetic Model by a Markov-Chain-Based Methodology. 555-562
Volume 64, Number 3, February 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Jinlu Zhang, Yin Fang, Xin Shao, Huajun Chen, Ningyu Zhang, Xiaohui Fan:
The Future of Molecular Studies through the Lens of Large Language Models. 563-566 - Anton Jansen, Noora Aho, Gerrit Groenhof, Pavel Buslaev, Berk Hess:
phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS. 567-574 - Tao Shen, Jiale Guo, Zunsheng Han, Gao Zhang, Qingxin Liu, Xinxin Si, Dongmei Wang, Song Wu, Jie Xia:
AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics. 575-583 - Mariona Torrens-Fontanals, Panagiotis Tourlas, Stefan Doerr, Gianni De Fabritiis:
PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data. 584-589 - Robert I. Horne, Jared Wilson-Godber, Alicia González Díaz, Z. Faidon Brotzakis, Srijit Seal, Rebecca C. Gregory, Andrea Possenti, Sean Chia, Michele Vendruscolo:
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity. 590-596 - Andre Nicolle, Sili Deng, Matthias Ihme, Nursulu Kuzhagaliyeva, Emad Al Ibrahim, Aamir Farooq:
Mixtures Recomposition by Neural Nets: A Multidisciplinary Overview. 597-620 - Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F. Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L. Brooks III, Nathalie Reuter:
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. 621-626 - Hongshuo Huang, Rishikesh Magar, Amir Barati Farimani:
Pretraining Strategies for Structure Agnostic Material Property Prediction. 627-637 - Surya Prakash Tiwari, Wei Shi, Samir Budhathoki, James Baker, Ali K. Sekizkardes, Lingxiang Zhu, Victor A. Kusuma, David P. Hopkinson, Janice A. Steckel:
Creation of Polymer Datasets with Targeted Backbones for Screening of High-Performance Membranes for Gas Separation. 638-652 - Gregory W. Kyro, Anton Morgunov, Rafael I. Brent, Victor S. Batista:
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. 653-665 - Hao Zhang, Jinchao Huang, Junjie Xie, Weifeng Huang, Yuedong Yang, Mingyuan Xu, Jinping Lei, Hongming Chen:
GRELinker: A Graph-Based Generative Model for Molecular Linker Design with Reinforcement and Curriculum Learning. 666-676 - Hyeonsu Kim, Kyunghoon Lee, Jun Hyeong Kim, Woo Youn Kim:
Deep Learning-Based Chemical Similarity for Accelerated Organic Light-Emitting Diode Materials Discovery. 677-689 - Lewis Y. Geer, Stephen E. Stein, William Gary Mallard, Douglas J. Slotta:
AIRI: Predicting Retention Indices and Their Uncertainties Using Artificial Intelligence. 690-696 - Prudencio Tossou, Cas Wognum, Michael Craig, Hadrien Mary, Emmanuel Noutahi:
Real-World Molecular Out-Of-Distribution: Specification and Investigation. 697-711 - Alec J. Sanchez, Sarah Maier, Krishnan Raghavachari:
Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning. 712-723 - Minfei Ma, Xinben Zhang, Liping Zhou, Zijian Han, Yulong Shi, Jintian Li, Leyun Wu, Zhijian Xu, Weiliang Zhu:
D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds. 724-736 - Weichen Bo, Yangqin Duan, Yurong Zou, Ziyan Ma, Tao Yang, Peng Wang, Tao Guo, Zhiyuan Fu, Jianmin Wang, Linchuan Fan, Jie liu, Taijin Wang, Lijuan Chen:
Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors. 737-748 - Susanta Das, Kenneth M. Merz Jr.:
Molecular Gas-Phase Conformational Ensembles. 749-760 - Qing Wang, Xuegang Fu, Yuting Yan, Tao Liu, Yuting Xie, Xiaoqing Song, Yu Zhou, Min Xu, Ping Wang, Peng Fu, Jianhui Huang, Niu Huang:
Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors. 761-774 - Justin K. Kirkland, Jugal Kumawat, Maliheh Shaban Tameh, Tyson Tolman, Allison C. Lambert, Graham R. Lief, Qing Yang, Daniel H. Ess:
Machine Learning Models for Predicting Zirconocene Properties and Barriers. 775-784 - Mingqiong Tong, Peng Liu, Chaoqun Li, Zhongyu Zhang, Wan Sun, Pingxuan Dong, Na Fan, Xiaoyue Wang, Jing Liu, Chao Lv, Zanxia Cao, Yan Wang:
Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. 785-798 - Jyotirmoy Deb, Lakshi Saikia, Kripa Dristi Dihingia, G. Narahari Sastry:
ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT. 799-811 - Luke Landry, Pengfei Li:
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. 812-824 - Christian Hölzer, Igor Gordiy, Stefan Grimme, Markus Bursch:
Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set. 825-836 - Shalmali Kharche, Manjul Yadav, Vrushali Hande, Shikha Prakash, Durba Sengupta:
Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. 837-850 - Xu Zhou, Zhiqiang Wei, Hao Lu, Jiaqi He, Yuan Gao, Xiaotong Hu, Cunji Wang, Yujie Dong, Hao Liu:
Large-Scale Molecular Dynamics Simulation Based on Heterogeneous Many-Core Architecture. 851-861 - Nurit Haspel, Hyunbum Jang, Ruth Nussinov:
Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics. 862-873 - Nopawit Khamto, Kraikrit Utama, Panida Boontawee, Atchara Janthong, Suriya Tatieng, Supakorn Arthan, Vachira Choommongkol, Padchanee Sangthong, Chavi Yenjai, Nuttee Suree, Puttinan Meepowpan:
Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLpro: Insights from the Computational and Experimental Investigations. 874-891 - Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, Toan T. Nguyen, Valerio Rizzi, Jörg B. Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossetti:
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. 892-904 - Sayyed Jalil Mahdizadeh, Michael Stier, Antonio Carlesso, Aurore Lamy, Melissa Thomas, Leif A. Eriksson:
Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase. 905-917 - Anna P. Tolstova, Alexander A. Makarov, Alexei A. Adzhubei:
Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. 918-932 - Christopher Kang, Alyson Shoji, Christophe Chipot, Rui Sun:
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs. 933-943 - Rajwinder Kaur, Stacey D. Wetmore:
Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. 944-959 - Ayse A. Bekar-Cesaretli, Omeir Khan, Thu Nguyen, Dima Kozakov, Diane Joseph-McCarthy, Sandor Vajda:
Conservation of Hot Spots and Ligand Binding Sites in Protein Models by AlphaFold2. 960-973 - Yunhao Mei, Yong Shen:
Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. 974-982 - Anupom Roy, Mikko Karttunen:
A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase. 983-1003 - Ian S. Knight, Olivier Mailhot, Khanh G. Tang, John J. Irwin:
DockOpt: A Tool for Automatic Optimization of Docking Models. 1004-1016 - Sana Akhter, Zhichao Tang, Jinan Wang, Mercy Haboro, Erik D. Holmstrom, Jingxin Wang, Yinglong Miao:
Mechanism of Ligand Binding to Theophylline RNA Aptamer. 1017-1029 - Zora Novakova, Zahra Aliakbar Tehrani, Radek Jurok, Lucia Motlova, Zsófia Kutil, Jiri Pavlicek, Shivam Shukla, Cindy J. Choy, Barbora Havlinova, Petra Baranova, Clifford E. Berkman, Martin Kuchar, Jirí Cerný, Cyril Barinka:
Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. 1030-1042 - Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu:
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. 1043-1049 - Jiashuo Zhang, Ruheng Wang, Leyi Wei:
MucLiPred: Multi-Level Contrastive Learning for Predicting Nucleic Acid Binding Residues of Proteins. 1050-1065 - Shuang Guo, Yuwei Liu, Yue Sun, Hanxiao Zhou, Yue Gao, Peng Wang, Hui Zhi, Yakun Zhang, Jing Gan, Shangwei Ning:
Metabolic-Related Gene Prognostic Index for Predicting Prognosis, Immunotherapy Response, and Candidate Drugs in Ovarian Cancer. 1066-1080 - Emma Goulard Coderc de Lacam, Benoît Roux, Christophe Chipot:
Classifying Protein-Protein Binding Affinity with Free-Energy Calculations and Machine Learning Approaches. 1081-1091 - Guolun Zhong, Lei Deng:
ACPScanner: Prediction of Anticancer Peptides by Integrated Machine Learning Methodologies. 1092-1104 - Farzad Molani, Simon Webb, Art E. Cho:
Correction to "Combining QM/MM Calculations with Classical Mining Minima to Predict Protein-Ligand Binding Free Energy". 1105 - Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn, Lonny R. Levin, Jochen Buck, Robert W. Myers, Stacia Kargman, Nigel Liverton, Peter T. Meinke, David J. Huggins:
Addition to "Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation". 1106
Volume 64, Number 4, February 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Ronaldo C. Prati, Bruno S. M. Rodrigues, Iberis Aragão, Thereza A. Soares, Marcos G. Quiles, Juarez L. F. Da Silva:
The Impact of Interdisciplinary, Gender and Geographic Distributions on the Citation Patterns of the Journal of Chemical Information and Modeling. 1107-1111 - Yanqiao Zhu, Dingshuo Chen, Yuanqi Du, Yingze Wang, Qiang Liu, Shu Wu:
Molecular Contrastive Pretraining with Collaborative Featurizations. 1112-1122 - Benson Chen, Mohammad M. Sultan, Theofanis Karaletsos:
Compositional Deep Probabilistic Models of DNA-Encoded Libraries. 1123-1133 - Seongwon Kim, Parisa Mollaei, Akshay Antony, Rishikesh Magar, Amir Barati Farimani:
GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models. 1134-1144 - Benjamin Kaufman, Edward C. Williams, Carl Underkoffler, Ryan Pederson, Narbe Mardirossian, Ian Watson, John Parkhill:
COATI: Multimodal Contrastive Pretraining for Representing and Traversing Chemical Space. 1145-1157 - Kathryn Klarich, Brian Goldman, Trevor Kramer, Patrick Riley, W. Patrick Walters:
Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases. 1158-1171 - Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter:
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. 1172-1186 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Band Gaps of Inorganic Materials Using a Gradient Boosted and Statistical Feature Selection Workflow. 1187-1200 - Frédéric Célerse, Matthew D. Wodrich, Sergi Vela, Simone Gallarati, Raimon Fabregat, Veronika Jurásková, Clémence Corminboeuf:
From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials. 1201-1212 - Mingyang Wang, Zhengjian Wu, Jike Wang, Gaoqi Weng, Yu Kang, Peichen Pan, Dan Li, Yafeng Deng, Xiaojun Yao, Zhitong Bing, Chang-Yu Hsieh, Tingjun Hou:
Genetic Algorithm-Based Receptor Ligand: A Genetic Algorithm-Guided Generative Model to Boost the Novelty and Drug-Likeness of Molecules in a Sampling Chemical Space. 1213-1228 - Juan F. Avellaneda-Tamayo, Ana L. Chávez-Hernández, Diana L. Prado-Romero, José L. Medina-Franco:
Chemical Multiverse and Diversity of Food Chemicals. 1229-1244 - Peter Ertl:
Database of 4 Million Medicinal Chemistry-Relevant Ring Systems. 1245-1250 - Chen Cheng, Paul Beroza:
Shape-Aware Synthon Search (SASS) for Virtual Screening of Synthon-Based Chemical Spaces. 1251-1260 - Yang Wang, Yi Zhou, Ke Du:
Enumeration, Nomenclature, and Stability Rules of Carbon Nanobelts. 1261-1276 - Andrew S. Lee, Sarah Elliott, Hassan Harb, Logan T. Ward, Ian T. Foster, Larry A. Curtiss, Rajeev S. Assary:
Emin: A First-Principles Thermochemical Descriptor for Predicting Molecular Synthesizability. 1277-1289 - Connor M. Davel, Timotej Bernat, Jeffrey R. Wagner, Michael R. Shirts:
Parameterization of General Organic Polymers within the Open Force Field Framework. 1290-1305 - José E. González, Rafael Besse, Matheus P. Lima, Juarez L. F. Da Silva:
Decoding Van der Waals Impact on Chirality Transfer in Perovskite Structures: Density Functional Theory Insights. 1306-1318 - Xiaojie Jin, Min Zhang, Beibei Fu, Mi Li, Jingyi Yang, Zhiming Zhang, Chenghao Li, Huijuan Zhang, Haibo Wu, Weiwei Xue, Yongqi Liu:
Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine. 1319-1330 - Colin L. Welsh, Lalima K. Madan:
Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. 1331-1346 - Akhil Kumar, Manisha Sharma, Harshwardhan H. Katkar:
Peripheral Linker Mediates Acyl Carrier Protein's Recognition of Dehydratase and Stabilizes Type-I Mycobacterium tuberculosis Fatty Acid Synthase. 1347-1360 - Imane Euldji, Widad Benmouloud, Kamil Paduszynski, Cherif Si-Moussa, Othmane Benkortbi:
Hybrid Improved Grey Wolf Support Vector Regression Algorithm for Modeling Solubilities of APIs in Pure Ionic Liquids: σ-Profile Descriptors. 1361-1376 - Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo:
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. 1377-1393 - Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu:
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. 1394-1406 - Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu:
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. 1407-1418
Volume 64, Number 5, March 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Marjolein T. Oostrom, Sean M. Colby, Thomas O. Metz:
DEIMoS GUI: An Open-Source User Interface for a High-Dimensional Mass Spectrometry Data Processing Tool. 1419-1424 - Ewelina Jamrozik, Marek Smieja, Sabina Podlewska:
ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation. 1425-1432 - Gao Tu, Tingting Fu, Guoxun Zheng, Binbin Xu, Rongpei Gou, Ding Luo, Panpan Wang, Weiwei Xue:
Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. 1433-1455 - Yunjiang Zhang, Shuyuan Li, Kong Meng, Shaorui Sun:
Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction. 1456-1472 - Juliette Martin:
AlphaFold2 Predicts Whether Proteins Interact Amidst Confounding Structural Compatibility. 1473-1480 - Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis:
Enhancing Protein-Ligand Binding Affinity Predictions Using Neural Network Potentials. 1481-1485 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Automatic Prediction of Peak Optical Absorption Wavelengths in Molecules Using Convolutional Neural Networks. 1486-1501 - Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng:
MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. 1502-1511 - Fernando Garcia-Escobar, Toshiaki Taniike, Keisuke Takahashi:
MonteCat: A Basin-Hopping-Inspired Catalyst Descriptor Search Algorithm for Machine Learning Models. 1512-1521 - Sung Wook Moon, Seung Kyu Min:
Gaussian Process Regression-Based Near-Infrared d-Luciferin Analogue Design Using Mutation-Controlled Graph-Based Genetic Algorithm. 1522-1532 - Pattipong Wisanpitayakorn, Sitanan Sartyoungkul, Alongkorn Kurilung, Yongyut Sirivatanauksorn, Wonnop Visessanguan, Nuankanya Sathirapongsasuti, Sakda Khoomrung:
Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data. 1533-1542 - Xiaohe Xu, Weijie Han, Xiangzhen Ning, Chengdong Zang, Chengcheng Xu, Chen Zeng, Chengtao Pu, Yanmin Zhang, Yadong Chen, Haichun Liu:
Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. 1543-1559 - Gregory A. Landrum, Sereina Riniker:
Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. 1560-1567 - Hatem Helal, Jesun Firoz, Jenna A. Bilbrey, Henry Sprueill, Kristina M. Herman, Mario Michael Krell, Tom Murray, Manuel Lopez Roldan, Mike Kraus, Ang Li, Payel Das, Sotiris S. Xantheas, Sutanay Choudhury:
Acceleration of Graph Neural Network-Based Prediction Models in Chemistry via Co-Design Optimization on Intelligence Processing Units. 1568-1580 - Camila M. Clemente, Juan M. Prieto, Marcelo A. Marti:
Unlocking Precision Docking for Metalloproteins. 1581-1592 - Giada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino:
Viral RNA Replication Suppression of SARS-CoV-2: Atomistic Insights into Inhibition Mechanisms of RdRp Machinery by ddhCTP. 1593-1604 - Jochem Nelen, Miguel Carmena-Bargueño, Carlos Martinez-Cortes, Alejandro Rodríguez-Martínez, José Manuel Villalgordo-Soto, Horacio Pérez Sánchez:
ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery. 1605-1614 - Tien-Sheng Tseng, Chao-Chang Lee, Po-Juei Chen, Chiu-Yuen Lin, Wang-Chuan Chen, Yu-Ching Lee, Jiun-Han Lin, Kaun-Wen Chen, Keng-Chang Tsai:
Structure-Guided Discovery of PD-1/PD-L1 Interaction Inhibitors: Peptide Design, Screening, and Optimization via Computation-Aided Phage Display Engineering. 1615-1627 - Dávid Zajacek, Adriána Dunárová, Lukás Bucinský, Marek Steklác:
Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate. 1628-1643 - Hong Ha Nguyen, Jim Tufts, David D. L. Minh:
On Inactivation of the Coronavirus Main Protease. 1644-1656 - Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker:
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. 1657-1681 - Giulia Cazzanelli, Andrea Dalle Vedove, Giovanni Spagnolli, Luca Terruzzi, Enrica Colasurdo, Alberto Boldrini, Alexandros Patsilinakos, Mattia Sturlese, Alessandro Grottesi, Emiliano Biasini, Alessandro Provenzani, Alessandro Quattrone, Graziano Lolli:
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains. 1682-1690 - Sebastian Anila, Sergey A. Samsonov:
Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes. 1691-1703 - Kaylen R. Meeks, Juan Ji, Mykola V. Protopopov, Olga O. Tarkhanova, Yurii S. Moroz, John J. Tanner:
Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography. 1704-1718 - Kun Wang, Ben Cao, Tao Ma, Yunzhu Zhao, Yanfen Zheng, Bin Wang, Shihua Zhou, Qiang Zhang:
Storing Images in DNA via base128 Encoding. 1719-1729 - Romanos Fasoulis, Maurício Menegatti Rigo, Gregory Lizée, Dinler A. Antunes, Lydia E. Kavraki:
APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. 1730-1750 - Zuojun Yang, Yuhan Wu, Hao Liu, Li He, Xiaoyuan Deng:
AMYGNN: A Graph Convolutional Neural Network-Based Approach for Predicting Amyloid Formation from Polypeptides. 1751-1762 - Nutaya Pravalphruekul, Maytus Piriyajitakonkij, Phond Phunchongharn, Supanida Piyayotai:
Correction to "De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder". 1763
Volume 64, Number 6, 2024
- Marta Pasquini, Marco Stenta:
LinChemIn: Route Arithmetic─Operations on Digital Synthetic Routes. 1765-1771 - Yulei Wang, Yuxiang Wang:
HBCalculator: A Tool for Hydrogen Bond Distribution Calculations in Molecular Dynamics Simulations. 1772-1777 - Kuo-Hao Lee, Lei Shi:
Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. 1778-1793 - Yidan Tang, Rocco Moretti, Jens Meiler:
Recent Advances in Automated Structure-Based De Novo Drug Design. 1794-1805 - Uddeshya Pandey, Sasi M. Behara, Siddhant Sharma, Rachit S. Patil, Souparnika Nambiar, Debasish Koner, Hussain Bhukya:
DeePNAP: A Deep Learning Method to Predict Protein-Nucleic Acid Binding Affinity from Their Sequences. 1806-1815 - Tuan Vinh, Loc Nguyen, Quang H. Trinh, Thanh-Hoang Nguyen-Vo, Binh P. Nguyen:
Predicting Cardiotoxicity of Molecules Using Attention-Based Graph Neural Networks. 1816-1827 - Hugo Rossignol, Michail Minotakis, Matteo Cobelli, Stefano Sanvito:
Machine-Learning-Assisted Construction of Ternary Convex Hull Diagrams. 1828-1840 - Yendrek Velásquez-López, Andrea Ruiz-Escudero, Sonia Arrasate, Humberto González Díaz:
Implementation of IFPTML Computational Models in Drug Discovery Against Flaviviridae Family. 1841-1852 - Eleftherios Christofi, Petra Bacová, Vagelis Harmandaris:
Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers. 1853-1867 - Javad Tayebi, Bagher Babaali:
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing. 1868-1881 - Zhonglin Cao, Simone Sciabola, Ye Wang:
Large-Scale Pretraining Improves Sample Efficiency of Active Learning-Based Virtual Screening. 1882-1891 - Ding Luo, Dandan Liu, Xiaoyang Qu, Lina Dong, Binju Wang:
Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. 1892-1906 - Derek P. Metcalf, Zachary L. Glick, Andrea Bortolato, Andy Jiang, Daniel L. Cheney, C. David Sherrill:
Directional ΔG Neural Network (DrΔG-Net): A Modular Neural Network Approach to Binding Free Energy Prediction. 1907-1918 - Vadim Korolev, Artem Mitrofanov:
Coarse-Grained Crystal Graph Neural Networks for Reticular Materials Design. 1919-1931 - Philipe Oliveira Fernandes, Anna Letícia Teotonio Dias, Valtair Severino dos Santos Júnior, Mateus Sá Magalhães Serafim, Yamara Viana Sousa, Gustavo Claro Monteiro, Isabel Duarte Coutinho, Marilia Valli, Marina Mol Sena Andrade Verzola, Flaviano Melo Ottoni, Rodrigo Maia de Pádua, Fernando Bombarda Oda, André Gustavo dos Santos, Adriano Defini Andricopulo, Vanderlan da Silva Bolzani, Bruno Eduardo Fernandes Mota, Ricardo José Alves, Renata Barbosa de Oliveira, Thales Kronenberger, Vinicius Gonçalves Maltarollo:
Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. 1932-1944 - Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang:
Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. 1945-1954 - Rohan Gorantla, Alzbeta Kubincová, Benjamin Suutari, Benjamin P. Cossins, Antonia S. J. S. Mey:
Benchmarking Active Learning Protocols for Ligand-Binding Affinity Prediction. 1955-1965 - Daniela Dolciami, Robert M. Ziolek, Daniel W. Davies, Michael Carter, N. Yi Mok, Richard Sherhod:
Exploiting Vector Pattern Diversity of Molecular Scaffolds for Cheminformatics Tasks in Drug Discovery. 1966-1974 - Mohammadamin Tavakoli, Ryan J. Miller, Mirana Angel, Michael A. Pfeiffer, Eugene S. Gutman, Aaron Mood, David Van Vranken, Pierre Baldi:
PMechDB: A Public Database of Elementary Polar Reaction Steps. 1975-1983 - Angel Jonathan Ruiz-Moreno, Raziel Cedillo-González, Luis Cordova-Bahena, Zhiqiang An, José L. Medina-Franco, Marco Velasco-Velázquez:
Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 Mpro Inhibitors from Large Chemical Libraries. 1984-1995 - Szymon Zdybel, Anita Sosnowska, Dominika Kowalska, Julia Sommer, Beate Conrady, Patrick Mester, Maciej Gromelski, Tomasz Puzyn:
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6. 1996-2007 - Justin Lübbers, Uta F. Lessel, Matthias Rarey:
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. 2008-2020 - Farag E. S. Mosa, Sara Alrawashdeh, Ayman O. S. El-Kadi, Khaled H. Barakat:
Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations. 2021-2034 - Shawn C. C. Hsueh, Mark Nijland, Adekunle Aina, Steven S. Plotkin:
Cyclization Scaffolding for Improved Vaccine Immunogen Stability: Application to Tau Protein in Alzheimer's Disease. 2035-2044 - Jacqueline C. Calderón, Passainte Ibrahim, Dorothea Gobbo, Francesco Luigi Gervasio, Timothy Clark:
Determinants of Neutral Antagonism and Inverse Agonism in the β2-Adrenergic Receptor. 2045-2057 - Wan Wei, Lloyd Wei Tat Tang, Ravi Kumar Verma, Hao Fan, Eric Chun Yong Chan:
Probe Substrate Dependencies in CYP3A4 Allosteric Inhibition: A Novel Molecular Mechanism Involving F-F′ Loop Perturbations. 2058-2067 - Amit Kumar, Harish Vashisth:
Quantitative Assessment of Energetic Contributions of Residues in a SARS-CoV-2 Viral Enzyme/Nanobody Interface. 2068-2076 - Matic Broz, Chris Oostenbrink, Urban Bren:
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. 2077-2083 - Omeir Khan, George Jones, Maria Lazou, Diane Joseph-McCarthy, Dima Kozakov, Dmitri Beglov, Sandor Vajda:
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. 2084-2100 - Sree Ganesh Balasubramani, Kseniia Korchagina, Steven Schwartz:
Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult? 2101-2111 - Huifeng Zhao, Dejun Jiang, Chao Shen, Jintu Zhang, Xujun Zhang, Xiaorui Wang, Dou Nie, Tingjun Hou, Yu Kang:
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein-Cyclic Peptide Complexes. 2112-2124
Volume 64, Number 7, 2024
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Bio-cheminformatics. 2125-2128 - Zoe Cournia, Christophe Chipot:
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. 2129-2131 - Deep Kumar Kirtania:
ChatGPT Generated Content and Similarity Index in Chemistry. 2132-2135 - Andrea Mauri, Matteo Bertola:
AlvaBuilder: A Software for De Novo Molecular Design. 2136-2142 - Michele Roggia, Benito Natale, Giorgio Amendola, Salvatore Di Maro, Sandro Cosconati:
Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach. 2143-2149 - Natalia Lapinska, Adam Paclawski, Jakub Szlek, Aleksander Mendyk:
SerotoninAI: Serotonergic System Focused, Artificial Intelligence-Based Application for Drug Discovery. 2150-2157 - Yuanyuan Zhang, Zengqian Deng, Xiaoyu Xu, Yinfei Feng, Junliang Shang:
Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review. 2158-2173 - Chao Pang, Jianbo Qiao, Xiangxiang Zeng, Quan Zou, Leyi Wei:
Deep Generative Models in De Novo Drug Molecule Generation. 2174-2194 - Benjamin Bouvier:
Substituted Oligosaccharides as Protein Mimics: Deep Learning Free Energy Landscapes. 2195-2204 - Xiangying Zhang, Haotian Gao, Haojie Wang, Zhihang Chen, Zhe Zhang, Xinchong Chen, Yan Li, Yifei Qi, Renxiao Wang:
PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction. 2205-2220 - Xiaoyi Li, Wenyan Qu, Jing Yan, Jianjun Tan:
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction. 2221-2235 - Tingzhong Tian, Shuya Li, Meng Fang, Dan Zhao, Jianyang Zeng:
MolSHAP: Interpreting Quantitative Structure-Activity Relationships Using Shapley Values of R-Groups. 2236-2249 - José Ferraz-Caetano, Filipe Teixeira, Dthenifer Cordeiro Santana:
Explainable Supervised Machine Learning Model To Predict Solvation Gibbs Energy. 2250-2262 - Xiaoyang Qu, Lina Dong, Ding Luo, Yubing Si, Binju Wang:
Water Network-Augmented Two-State Model for Protein-Ligand Binding Affinity Prediction. 2263-2274 - Miriana Di Stefano, Salvatore Galati, Lisa Piazza, Carlotta Granchi, Simone Mancini, Filippo Fratini, Marco Macchia, Giulio Poli, Tiziano Tuccinardi:
VenomPred 2.0: A Novel In Silico Platform for an Extended and Human Interpretable Toxicological Profiling of Small Molecules. 2275-2289 - Zheng Fang, Zhongqi Wu, Xinbo Wu, Shixin Chen, Xing Wang, Saurabh Umrao, Abhisek Dwivedy:
APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions. 2290-2301 - Ying Zhou, Ting Qi, Min Pan, Jing Tu, Xiangwei Zhao, Qinyu Ge, Zuhong Lu:
Deep-Cloud: A Deep Neural Network-Based Approach for Analyzing Differentially Expressed Genes of RNA-seq Data. 2302-2310 - Aaron R. Flanagan, Frank G. Glavin:
A Comparative Analysis of Data Synthesis Techniques to Improve Classification Accuracy of Raman Spectroscopy Data. 2311-2322 - Ghaith Mqawass, Petr Popov:
graphLambda: Fusion Graph Neural Networks for Binding Affinity Prediction. 2323-2330 - Wouter Heyndrickx, Lewis H. Mervin, Tobias Morawietz, Noé Sturm, Lukas Friedrich, Adam Zalewski, Anastasia Pentina, Lina Humbeck, Martijn Oldenhof, Ritsuya Niwayama, Peter Schmidtke, Nikolas Fechner, Jaak Simm, Adam Arany, Nicolas Drizard, Rama Jabal, Arina Afanasyeva, Regis Loeb, Shlok Verma, Simon Harnqvist, Matthew Holmes, Balazs Pejo, Maria Telenczuk, Nicholas Holway, Arne Dieckmann, Nicola Rieke, Friederike Zumsande, Djork-Arné Clevert, Michael Krug, Christopher N. Luscombe, Darren V. S. Green, Peter Ertl, Peter Antal, David Marcus, Nicolas Do Huu, Hideyoshi Fuji, Stephen D. Pickett, Gergely Ács, Eric Boniface, Bernd Beck, Yax Sun, Arnaud Gohier, Friedrich Rippmann, Ola Engkvist, Andreas H. Göller, Yves Moreau, Mathieu N. Galtier, Ansgar Schuffenhauer, Hugo Ceulemans:
MELLODDY: Cross-pharma Federated Learning at Unprecedented Scale Unlocks Benefits in QSAR without Compromising Proprietary Information. 2331-2344 - Yuki Matsukiyo, Chikashige Yamanaka, Yoshihiro Yamanishi:
De Novo Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization. 2345-2355 - Gianmattia Sgueglia, Michail D. Vrettas, Marco Chino, Alfonso De Simone, Angela Lombardi:
MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks. 2356-2367 - Ewerton Cristhian Lima de Oliveira, Hannah Hirmz, Evelien Wynendaele, Juliana Auzier Seixas Feio, Igor Matheus Souza Moreira, Kauê Santana da Costa, Anderson H. Lima, Bart De Spiegeleer, Claudomiro de Souza de Sales Junior:
BrainPepPass: A Framework Based on Supervised Dimensionality Reduction for Predicting Blood-Brain Barrier-Penetrating Peptides. 2368-2382 - Hongle An, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids. 2383-2392 - Changjiang Li, Quan Zou, Cangzhi Jia, Jia Zheng:
AMPpred-MFA: An Interpretable Antimicrobial Peptide Predictor with a Stacking Architecture, Multiple Features, and Multihead Attention. 2393-2404 - Sean Cottrell, Rui Wang, Guo-Wei Wei:
PLPCA: Persistent Laplacian-Enhanced PCA for Microarray Data Analysis. 2405-2420 - Samuel Goldman, Jiayi Xin, Joules Provenzano, Connor W. Coley:
MIST-CF: Chemical Formula Inference from Tandem Mass Spectra. 2421-2431 - Hyeongwoo Kim, Kyunghoon Lee, Chansu Kim, Jaechang Lim, Woo Youn Kim:
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening. 2432-2444 - Tzu-Hsien Yang, Jhih-Cheng Chen, Yuan-Han Lee, Shang-Yi Lu, Sheng-Hang Wu, Fang-Yuan Chang, Yan-Cheng Huang, Mei-Hsien Lee, Yan-Yuan Tseng, Wei-Sheng Wu:
Identifying Human miRNA Target Sites via Learning the Interaction Patterns between miRNA and mRNA Segments. 2445-2453 - Xuelian Li, Cheng Shen, Hui Zhu, Yujian Yang, Qing Wang, Jincai Yang, Niu Huang:
A High-Quality Data Set of Protein-Ligand Binding Interactions Via Comparative Complex Structure Modeling. 2454-2466 - Nieves C. Comelli, Patricia A. Diez, María R. Rodríguez, Gabriel O. Denett, Tamara E. López, Daniela M. Bracamonte, Erlinda V. Ortiz, Diego A. Sampietro, Pablo R. Duchowicz:
Excito-repellent and Pesticide-Likeness Properties of Essential Oils on Carpophilus dimidiatus (Fabricius) (Nitidulidae) and Oryzaephilus mercator (L.) (Silvanidae). 2467-2487 - Michael Brocidiacono, Paul G. Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha:
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. 2488-2495 - Rohan Gorantla, Alzbeta Kubincová, Andrea Y. Weiße, Antonia S. J. S. Mey:
From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction. 2496-2507 - Chaoshu Duan, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Interpretable Perturbator for Variable Selection in near-Infrared Spectral Analysis. 2508-2514 - Issar Arab, Kristof Egghe, Kris Laukens, Ke Chen, Khaled H. Barakat, Wout Bittremieux:
Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. 2515-2527 - Zhaoyang Chen, Le Zhang, Pei Zhang, Huizhu Guo, Ruiqiu Zhang, Ling Li, Xiao Li:
Prediction of Cytochrome P450 Inhibition Using a Deep Learning Approach and Substructure Pattern Recognition. 2528-2538 - Emma Svensson, Pieter-Jan Hoedt, Sepp Hochreiter, Günter Klambauer:
HyperPCM: Robust Task-Conditioned Modeling of Drug-Target Interactions. 2539-2553 - Junjie Xie, Sheng Chen, Jinping Lei, Yuedong Yang:
DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model. 2554-2564 - Henrique Barbosa, Gabriel Zarzana Espinoza, Maiara Amaral, Erica Valadares de Castro Levatti, Mariana Babberg Abiuzi, Gabriel Corrêa Veríssimo, Philipe de Oliveira Fernandes, Vinicius Gonçalves Maltarollo, Andre Gustavo Tempone, Káthia Maria Honório, João Henrique Ghilardi Lago:
Andrographolide: A Diterpenoid from Cymbopogon schoenanthus Identified as a New Hit Compound against Trypanosoma cruzi Using Machine Learning and Experimental Approaches. 2565-2576 - Fatemeh Rafiei, Hojjat Zeraati, Karim Abbasi, Parvin Razzaghi, Jahan B. Ghasemi, Mahboubeh Parsaeian, Ali Masoudi-Nejad:
CFSSynergy: Combining Feature-Based and Similarity-Based Methods for Drug Synergy Prediction. 2577-2585 - Katarzyna Kapuscinska, Zofia Dukala, Mekhola Doha, Eman Ansari, Jimin Wang, Gary W. Brudvig, Bernand Brooks, Muhamed Amin:
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. 2586-2593 - Andreas Zamanos, George Ioannakis, Ioannis Z. Emiris:
HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures. 2594-2611 - Egor Marin, Margarita Kovaleva, Maria Kadukova, Khalid Mustafin, Polina Khorn, Andrey Rogachev, Alexey Mishin, Albert Guskov, Valentin Borshchevskiy:
Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking. 2612-2623 - Thomas M. Whitehead, Joel Strickland, Gareth John Conduit, Alexandre Borrel, Daniel Mucs, Irene Baskerville-Abraham:
Quantifying the Benefits of Imputation over QSAR Methods in Toxicology Data Modeling. 2624-2636 - Zachary Smith, Michael Strobel, Bodhi P. Vani, Pratyush Tiwary:
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. 2637-2644 - Linwei Sai, Li Fu, Jijun Zhao:
Predicting Binding Energies and Electronic Properties of Boron Nitride Fullerenes Using a Graph Convolutional Network. 2645-2653 - Xin Feng, Zhansen Ma, Cuinan Yu, Ruihao Xin:
MRNDR: Multihead Attention-Based Recommendation Network for Drug Repurposing. 2654-2669 - Yi He, Kaifeng Liu, Xiangyu Yu, Hengzheng Yang, Weiwei Han:
Building a Kokumi Database and Machine Learning-Based Prediction: A Systematic Computational Study on Kokumi Analysis. 2670-2680 - Niccolo Alberto Elia Venanzi, Andrea Basciu, Attilio Vittorio Vargiu, Alexandros Kiparissides, Paul A. Dalby, Duygu Dikicioglu:
Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. 2681-2694 - William J. Godinez, Vladimir Trifonov, Bin Fang, Guray Kuzu, Luying Pei, W. Armand Guiguemde, Eric J. Martin, Frederick J. King, Jeremy L. Jenkins, Peter Skewes-Cox:
Compound Activity Prediction with Dose-Dependent Transcriptomic Profiles and Deep Learning. 2695-2704 - Subhojit Paul, Kaushika Olymon, Gustavo Sganzerla Martinez, Sharmilee Sarkar, Venkata Rajesh Yella, Aditya Kumar:
MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI. 2705-2719 - Wei Zhang, Minjie Mou, Wei Hu, Mingkun Lu, Hanyu Zhang, Hongning Zhang, Yongchao Luo, Hongquan Xu, Lin Tao, Haibin Dai, Jianqing Gao, Feng Zhu:
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery. 2720-2732 - Jiashun Mao, Jianmin Wang, Amir Zeb, Kwang-Hwi Cho, Haiyan Jin, Jongwan Kim, Onju Lee, Yunyun Wang, Kyoung Tai No:
Transformer-Based Molecular Generative Model for Antiviral Drug Design. 2733-2745 - Tong Xie, Yuwei Wan, Haoran Wang, Ina Østrøm, Shaozhou Wang, Mingrui He, Rong Deng, Xinyuan Wu, Clara Grazian, Chunyu Kit, Bram Hoex:
Opinion Mining by Convolutional Neural Networks for Maximizing Discoverability of Nanomaterials. 2746-2759 - Pawan Panwar, Quanpeng Yang, Ashlie Martini:
Temperature-Dependent Density and Viscosity Prediction for Hydrocarbons: Machine Learning and Molecular Dynamics Simulations. 2760-2774 - Pablo Rodríguez-Belenguer, Victor Mangas-Sanjuan, Emilio Soria-Olivas, Manuel Pastor:
Integrating Mechanistic and Toxicokinetic Information in Predictive Models of Cholestasis. 2775-2788 - Bodhi P. Vani, Akashnathan Aranganathan, Pratyush Tiwary:
Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE. 2789-2797 - Rui Wang, Zhecheng Zhou, Xiaonan Wu, Xin Jiang, Linlin Zhuo, Mingzhe Liu, Hao Li, Xiangzheng Fu, Xiaojun Yao:
An Effective Plant Small Secretory Peptide Recognition Model Based on Feature Correction Strategy. 2798-2806 - Xuetong Yang, Junru Jin, Ruheng Wang, Zhongshen Li, Yu Wang, Leyi Wei:
CACPP: A Contrastive Learning-Based Siamese Network to Identify Anticancer Peptides Based on Sequence Only. 2807-2816 - Tingjun Xu, Wenxing Gao, Lixin Zhu, Wanning Chen, Chaoqun Niu, Wenjing Yin, Liangxiao Ma, Xinyue Zhu, Yunchao Ling, Sheng Gao, Lei Liu, Na Jiao, Weiming Chen, Guoqing Zhang, Ruixin Zhu, Dingfeng Wu:
NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease. 2817-2828 - Yuta Hozumi, Kiyoto Aramis Tanemura, Guo-Wei Wei:
Preprocessing of Single Cell RNA Sequencing Data Using Correlated Clustering and Projection. 2829-2838 - Ruihao Xin, Fan Zhang, Jiaxin Zheng, Yangyi Zhang, Cuinan Yu, Xin Feng:
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives. 2839-2853 - Tianshuo Wang, Ruheng Wang, Leyi Wei:
AttenSyn: An Attention-Based Deep Graph Neural Network for Anticancer Synergistic Drug Combination Prediction. 2854-2862 - Jian He, Menglong Li, Jiangguo Qiu, Xuemei Pu, Yanzhi Guo:
HOPEXGB: A Consensual Model for Predicting miRNA/lncRNA-Disease Associations Using a Heterogeneous Disease-miRNA-lncRNA Information Network. 2863-2877 - Kai-Yang Zhong, Meng-Liang Wen, Fan-Fang Meng, Xin Li, Bei Jiang, Xin Zeng, Yi Li:
MMDTA: A Multimodal Deep Model for Drug-Target Affinity with a Hybrid Fusion Strategy. 2878-2888 - Haibin Li, Jun Meng, Zhaowei Wang, Youwei Tang, Shihao Xia, Yu Wang, Zhaojing Qin, Yushi Luan:
miPEPPred-FRL: A Novel Method for Predicting Plant MiRNA-Encoded Peptides Using Adaptive Feature Representation Learning. 2889-2900 - Shijie Xu, Akira Onoda:
Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning. 2901-2911 - Tao Wang, Wentao Wang, Xin Jiang, Jiaxing Mao, Linlin Zhuo, Mingzhe Liu, Xiangzheng Fu, Xiaojun Yao:
ML-NPI: Predicting Interactions between Noncoding RNA and Protein Based on Meta-Learning in a Large-Scale Dynamic Graph. 2912-2920 - Ziqiao Zhang, Yatao Bian, Ailin Xie, Pengju Han, Shuigeng Zhou:
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery? 2921-2930
Volume 64, Number 8, 2024
- Tarak Karmakar, Thereza A. Soares, Kenneth M. Merz Jr.:
Enhancing Coarse-Grained Models through Machine Learning. 2931-2932 - Zhitao Cai, Hao Peng, Shuo Sun, Jiahao He, Fangfang Luo, Yandong Huang:
DeepKa Web Server: High-Throughput Protein pKa Prediction. 2933-2940 - Keda Yang, Zewen Xie, Zhen Li, Xiaoliang Qian, Nannan Sun, Tao He, Zuodong Xu, Jing Jiang, Qi Mei, Jie Wang, Shugang Qu, Xiaoling Xu, Chaoxiang Chen, Bin Ju:
MolProphet: A One-Stop, General Purpose, and AI-Based Platform for the Early Stages of Drug Discovery. 2941-2947 - Babak A. Mahjour, Connor W. Coley:
RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries. 2948-2954 - Yuheng Ding, Bo Qiang, Qixuan Chen, Yiqiao Liu, Liangren Zhang, Zhenming Liu:
Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective. 2955-2970 - Lorenza Pirona, Federico Ballabio, Mercedes Alfonso-Prieto, Riccardo Capelli:
Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. 2971-2978 - Damla Ovek, Ozlem Keskin, Attila Gürsoy:
ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations. 2979-2987 - David C. Williams, Neil Inala:
Physics-Informed Generative Model for Drug-like Molecule Conformers. 2988-3007 - Maxwell C. Venetos, Masha Elkin, Connor Delaney, John F. Hartwig, Kristin A. Persson:
Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures. 3008-3020 - Annie M. Westerlund, Siva Manohar Koki, Supriya Kancharla, Alessandro Tibo, Lakshidaa Saigiridharan, Mikhail Kabeshov, Rocío Mercado, Samuel Genheden:
Do Chemformers Dream of Organic Matter? Evaluating a Transformer Model for Multistep Retrosynthesis. 3021-3033 - Hazem Mslati, Francesco Gentile, Mohit Pandey, Fuqiang Ban, Artem Cherkasov:
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. 3034-3046 - Zhihao Gu, Yong Yan, Hanwen Liu, Di Wu, Hequan Yao, Kejiang Lin, Xuanyi Li:
Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network. 3047-3058 - Miguel Gallegos, Bienfait Kabuyaya Isamura, Paul L. A. Popelier, Ángel Martín Pendás:
An Unsupervised Machine Learning Approach for the Automatic Construction of Local Chemical Descriptors. 3059-3079 - Jianing Fan, Shao-Hua Shi, Hong Xiang, Li Fu, Yanjing Duan, Dong-Sheng Cao, Hongwei Lu:
Predicting Elimination of Small-Molecule Drug Half-Life in Pharmacokinetics Using Ensemble and Consensus Machine Learning Methods. 3080-3092 - Ida Rahu, Meelis Kull, Anneli Kruve:
Predicting the Activity of Unidentified Chemicals in Complementary Bioassays from the HRMS Data to Pinpoint Potential Endocrine Disruptors. 3093-3104 - Lei Song, Huimin Zhu, Kaili Wang, Min Li:
LGGA-MPP: Local Geometry-Guided Graph Attention for Molecular Property Prediction. 3105-3113 - Sebastian Schieferdecker, Florian Rottach, Esther Vock:
In Silico Prediction of Oral Acute Rodent Toxicity Using Consensus Machine Learning. 3114-3122 - Xiangwen Wang, Derek Quinn, Thomas S. Moody, Meilan Huang:
ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes. 3123-3139 - Hongni Jin, Kenneth M. Merz Jr.:
Modeling Zinc Complexes Using Neural Networks. 3140-3148 - Jiamin Chang, Xiaoyu Fan, Boxue Tian:
DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation. 3149-3160 - Mustafa Kemal Ozalp, Patricia A. Vignaux, Ana C. Puhl, Thomas R. Lane, Fabio Urbina, Sean Ekins:
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors. 3161-3172 - Ramil I. Nugmanov:
PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding. 3173-3179 - Martin Priessner, Richard J. Lewis, Magnus J. Johansson, Jonathan M. Goodman, Jon Paul Janet, Anna Tomberg:
HSQC Spectra Simulation and Matching for Molecular Identification. 3180-3191 - Maria José Tenorio, Miguel Á. González, Julia D. Magdaleno, Inmaculada Suárez, Baudilio Coto:
Viscosities and Densities of Binary and Ternary Mixtures of Aliphatic and Polyaromatic Hydrocarbons: Pyrene +1-Methylnaphthalene + Dodecane at T = (293.15 to 343.15) K. Experiment and Modeling. 3192-3204 - Taketomo Isazawa, Jacqueline M. Cole:
How Beneficial Is Pretraining on a Narrow Domain-Specific Corpus for Information Extraction about Photocatalytic Water Splitting? 3205-3212 - Daimon Sakaguchi, Hiroaki Gotoh:
Using Three-Dimensional Information to Predict and Interpret the Facial Selectivities of Nucleophilic Additions to Cyclic Ketones. 3213-3221 - Teng-Zhi Long, Dejun Jiang, Shao-Hua Shi, You-Chao Deng, Wen-Xuan Wang, Dong-Sheng Cao:
Enhancing Multi-species Liver Microsomal Stability Prediction through Artificial Intelligence. 3222-3236 - Shreya Bhattacharya, Priyadarshi Satpati:
Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes? 3237-3247 - Didier Desmecht, Vincent Dubois:
Correlation of the Molecular Cross-Sectional Area of Organic Monofunctional Compounds with Topological Descriptors. 3248-3259 - Shivam Parashar, Alexander V. Neimark:
Pore Structure Compartmentalization for Advanced Characterization of Metal-Organic Framework Materials. 3260-3268 - Luis Macaya, Duván González, Esteban Vöhringer-Martinez:
Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant. 3269-3277 - Felipe L. Oliveira, Pierre M. Esteves:
pyCOFBuilder: A Python Package for Automated Creation of Covalent Organic Framework Models Based on the Reticular Approach. 3278-3289 - Valentin Milia, Nathalie Tarrat, Christophe Zanon, Juan Cortés, Mathias Rapacioli:
Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates. 3290-3301 - Arkadiusz Leniak, Wojciech Pietrus, Rafal Kurczab:
From NMR to AI: Designing a Novel Chemical Representation to Enhance Machine Learning Predictions of Physicochemical Properties. 3302-3321 - Rodrigo A. Cormanich, Gabriel D. da Silva:
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations. 3322-3331 - Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey:
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. 3332-3349 - Ander Francisco Pereira, Leandro Martínez:
Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. 3350-3359 - Satyabrata Majumder, Giuseppe Deganutti, Ludovico Pipitò, Dwaipayan Chaudhuri, Joyeeta Datta, Kalyan Giri:
Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling. 3360-3374 - Nicolas Chéron:
Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase. 3375-3385 - Yu Zou, Lulu Guan, Jingwang Tan, Bote Qi, Yunxiang Sun, Fengjuan Huang, Qingwen Zhang:
Molecular Insights into the Differential Effects of Acetylation on the Aggregation of Tau Microtubule-Binding Repeats. 3386-3399 - Ru-De Lin, Xiu Xing, Yuan Yu, Wen-Dian Li, Dan-Dan Chang, Fei-Yan Tao, Na Wang:
Theoretical Analysis of Selectivity Differences in Ketoreductases toward Aldehyde and Ketone Carbonyl Groups. 3400-3410 - Jiaojiao Wang, Ting Ren, Guohui Sun, Na Zhang, Lijiao Zhao, Rugang Zhong:
Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation. 3411-3429 - Filipe E. P. Rodrigues, Tamis Darbre, Miguel Machuqueiro:
High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion. 3430-3442 - Rafael Giordano Viegas, Ingrid B. S. Martins, Murilo Nogueira Sanches, Antonio B. Oliveira Junior, Juliana B. de Camargo, Fernando V. Paulovich, Vitor B. P. Leite:
ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization. 3443-3450 - Yanjun Feng, Changda Gong, Jieyu Zhu, Guixia Liu, Yun Tang, Weihua Li:
Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. 3451-3464 - Luis J. Walter, Patrick K. Quoika, Martin Zacharias:
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations. 3465-3476 - Riya Samanta, Xinhao Zhuang, Kristen M. Varney, David J. Weber, Silvina Matysiak:
Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator. 3477-3487 - Angela M. Barragan, Kyle Ghaby, Matthew P. Pond, Benoît Roux:
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. 3488-3502 - Tian Hua Wang, Haiping Shao, Bingqiang Zhao, Hong Lin Zhai:
Molecular Insights into the Variability in Infection and Immune Evasion Capabilities of SARS-CoV-2 Variants: A Sequence and Structural Investigation of the RBD Domain. 3503-3523 - Tengyu Xie, Jing Huang:
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? 3524-3536 - Yi Zhang, Xuanzhao Li:
Empowering Graph Neural Networks with Block-Based Dual Adaptive Deep Adjustment for Drug Resistance-Related NcRNA Discovery. 3537-3547 - Lianci Tao, Tong Zhou, Zhixiang Wu, Fangrui Hu, Shuang Yang, Xiaotian Kong, Chunhua Li:
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein-DNA Interaction Hotspots. 3548-3557 - Zhe Su, Yiying Tong, Guo-Wei Wei:
Hodge Decomposition of Single-Cell RNA Velocity. 3558-3568 - Ping Xuan, Siyuan Lu, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Tiangang Zhang:
Learning Association Characteristics by Dynamic Hypergraph and Gated Convolution Enhanced Pairwise Attributes for Prediction of Disease-Related lncRNAs. 3569-3578 - Hongyan Chen, Dongxue Yan, Jie Sun, Meng Zhou:
Inference of Developmental Hierarchy and Functional States of Exhausted T Cells from Epigenetic Profiles with Deep Learning. 3579-3591 - Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud:
Addition to "Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model". 3592
Volume 64, Number 9, 2024
- Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov:
DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories. 3593-3598 - Pengchao Zhang, Axel Tosello Gardini, Xuefei Xu, Michele Parrinello:
Intramolecular and Water Mediated Tautomerism of Solvated Glycine. 3599-3604 - Stefan Boresch:
On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations. 3605-3609 - Maksim Kuznetsov, Fedor Ryabov, Roman Schutski, Rim Shayakhmetov, Yen-Chu Lin, Alex Aliper, Daniil Polykovskiy:
COSMIC: Molecular Conformation Space Modeling in Internal Coordinates with an Adversarial Framework. 3610-3620 - Hajime Shimakawa, Akiko Kumada, Masahiro Sato:
Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties. 3621-3629 - Shukai Gu, Yuwei Yang, Yihao Zhao, Jiayue Qiu, Xiaorui Wang, Henry Hoi Yee Tong, Liwei Liu, Xiaozhe Wan, Huanxiang Liu, Tingjun Hou, Yu Kang:
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios. 3630-3639 - Da-zhou Li, Xin Xu, Jia-heng Pan, Wei Gao, Shi-rui Zhang:
Image2InChI: Automated Molecular Optical Image Recognition. 3640-3649 - Bingxin Zhou, Lirong Zheng, Banghao Wu, Yang Tan, Outongyi Lv, Kai Yi, Guisheng Fan, Liang Hong:
Protein Engineering with Lightweight Graph Denoising Neural Networks. 3650-3661 - Koichi Handa, Saki Yoshimura, Michiharu Kageyama, Takeshi Iijima:
Development of Novel Methods for QSAR Modeling by Machine Learning Repeatedly: A Case Study on Drug Distribution to Each Tissue. 3662-3669 - Moritz Walter, Samuel J. Webb, Valerie J. Gillet:
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features. 3670-3688 - Yu Pang, Yihao Chen, Mujie Lin, Yanhong Zhang, Jiquan Zhang, Ling Wang:
MMSyn: A New Multimodal Deep Learning Framework for Enhanced Prediction of Synergistic Drug Combinations. 3689-3705 - Yu Zhu, Jing Gu, Zhuoran Zhao, A. W. Edith Chan, Maria F. Mojica, Andrea M. Hujer, Robert A. Bonomo, Shozeb M. Haider:
Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning. 3706-3717 - Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song:
FraHMT: A Fragment-Oriented Heterogeneous Graph Molecular Generation Model for Target Proteins. 3718-3732 - Vincenzo Vigna, Tânia F. G. G. Cova, Sandra C. C. Nunes, A. A. C. C. Pais, Emilia Sicilia:
Machine Learning-Based Prediction of Reduction Potentials for PtIV Complexes. 3733-3743 - Haopeng Ai, Deyin Wu, Huihao Zhou, Jun Xu, Qiong Gu:
dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks. 3744-3755 - Tzu-Hsien Yang:
DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning. 3756-3766 - Otávio L. Santana, Daniel G. Silva, Sidney R. Santana:
Solvate Suite: A Command-Line Interface for Molecular Simulations and Multiscale Microsolvation Modeling. 3767-3778 - Boyang Ni, Haoying Wang, Huda Kadhim Salem Khalaf, Vincent Blay, Douglas R. Houston:
AutoDock-SS: AutoDock for Multiconformational Ligand-Based Virtual Screening. 3779-3789 - Daniel S. Wigh, Joe Arrowsmith, Alexander Pomberger, Kobi C. Felton, Alexei A. Lapkin:
ORDerly: Data Sets and Benchmarks for Chemical Reaction Data. 3790-3798 - Marzieh Saeedimasine, Roja Rahmani, Alexander P. Lyubartsev:
Biomolecular Adsorption on Nanomaterials: Combining Molecular Simulations with Machine Learning. 3799-3811 - Pieter Buys Burger, Xiaohu Hu, Ilya Balabin, Morné Muller, Megan Stanley, Fourie Joubert, Thomas M. Kaiser:
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology. 3812-3825 - Rohan Chandraghatgi, Hai-Feng Ji, Gail L. Rosen, Bahrad A. Sokhansanj:
Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening. 3826-3840 - Sankar Maity, Somdev Pahari, Santanu Santra, Madhurima Jana:
Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. 3841-3854 - Dulce C. Guzmán-Ocampo, Rodrigo Aguayo-Ortiz, Laura Dominguez:
Understanding the Modulatory Role of E2012 on the γ-Secretase-Substrate Interaction. 3855-3864 - David Ferro-Costas, Pedro A. Sánchez-Murcia, Antonio Fernández-Ramos:
Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation. 3865-3873 - Lina Zhao, Yanjiao Wang, Yi Zhang, Hao Chen, Fude Sun:
Dynamic Simulations of Interaction of the PEG-DPPE Micelle-Encapsulated Short-Chain Ceramides with the Raft-Included Membrane. 3874-3883 - Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi:
Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model. 3884-3895 - Zhengyue Zhang, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer, Petr Stadlbauer:
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. 3896-3911 - Paige E. Bowling, Saswata Dasgupta, John M. Herbert:
Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. 3912-3922 - Krishnendu Sinha, Ipsita Basu, Zacharia Shah, Salim Shah, Suman Chakrabarty:
Leveraging Bidirectional Nature of Allostery To Inhibit Protein-Protein Interactions (PPIs): A Case Study of PCSK9-LDLR Interaction. 3923-3932 - Ying Zheng, Nianhang Chen, Zhongju Ji, Qiongyu Ye, Pingping Huang, Xiaodie Chen, Guanghong Cui, Lixin Duan, Fan Zhang:
Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site. 3933-3941 - Mueed Ur Rahman, Saira Bano, Xiaokun Hong, Ruo-Xu Gu, Hai-Feng Chen:
Early Aggregation Mechanism of SOD128-38 Based on Force Field Parameter of 5-Cyano-Tryptophan. 3942-3952 - Dhiman Ray, Sudip Das, Umberto Raucci:
Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. 3953-3958
Volume 64, Number 10, 2024
- Issue Editorial Masthead.
- Issue Publication Information.
- Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Materials Science. 3959-3960 - Petrina Kamya, Ivan V. Ozerov, Frank W. Pun, Kyle Tretina, Tatyana Fokina, Shan Chen, Vladimir Naumov, Xi Long, Sha Lin, Mikhail Korzinkin, Daniil Polykovskiy, Alex Aliper, Feng Ren, Alex Zhavoronkov:
PandaOmics: An AI-Driven Platform for Therapeutic Target and Biomarker Discovery. 3961-3969 - Yueqing Zhang, Zhihan Zhang, Dongliang Ke, Xiaolin Pan, Xingyu Wang, Xudong Xiao, Changge Ji:
FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints. 3970-3976 - Zishuo Cheng, Mahesh Aitha, Caitlyn A. Thomas, Aidan Sturgill, Mitch Fairweather, Amy Hu, Christopher R. Bethel, Dann D. Rivera, Patricia Dranchak, Pei W. Thomas, Han Li, Qi Feng, Kaicheng Tao, Minshuai Song, Na Sun, Shuo Wang, Surendra Bikram Silwal, Richard C. Page, Walt Fast, Robert A. Bonomo, Maria Weese, Waldyn G. Martinez, James Inglese, Michael W. Crowder:
Machine Learning Models Identify Inhibitors of New Delhi Metallo-β-lactamase. 3977-3991 - Payam Kelich, Jaquesta Adams, Sanghwa Jeong, Nicole Navarro, Markita P. Landry, Lela Vukovic:
Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths. 3992-4001 - Ting Qi, Ying Zhou, Yuqi Sheng, Zhihui Li, Yuwei Yang, Quanjun Liu, Qinyu Ge:
Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning. 4002-4008 - Michael Backenköhler, Joschka Groß, Verena Wolf, Andrea Volkamer:
Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases. 4009-4020 - Ronen Taub, Yonatan Savir:
SAF: Smart Aggregation Framework for Revealing Atoms Importance Rank and Improving Prediction Rates in Drug Discovery. 4021-4030 - Hosein Fooladi, Steffen Hirte, Johannes Kirchmair:
Quantifying the Hardness of Bioactivity Prediction Tasks for Transfer Learning. 4031-4046 - Juan S. Grassano, Ignacio Pickering, Adrian E. Roitberg, Mariano C. González Lebrero, Dario A. Estrin, Jonathan Alexis Semelak:
Assessment of Embedding Schemes in a Hybrid Machine Learning/Classical Potentials (ML/MM) Approach. 4047-4058 - Rongpei Gou, Jingyi Yang, Menghan Guo, Yingjun Chen, Weiwei Xue:
CNSMolGen: A Bidirectional Recurrent Neural Network-Based Generative Model for De Novo Central Nervous System Drug Design. 4059-4070 - Vishal Dey, Xia Ning:
Improving Anticancer Drug Selection and Prioritization via Neural Learning to Rank. 4071-4088 - Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks III:
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. 4089-4101 - Renxiu Song, Kaifeng Liu, Qizheng He, Fei He, Weiwei Han:
Exploring Bitter and Sweet: The Application of Large Language Models in Molecular Taste Prediction. 4102-4111 - Mehdi Sahihi, Pierre Fayon, Lionel Nauton, Florent Goujon, Julien Devémy, Alain Dequidt, Patrice Hauret, Patrice Malfreyt:
Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability. 4112-4120 - Sonia Kumari, Masilamani Elizabeth Sobhia:
Targeting an Old Foe for Cancer: A Molecular Dynamics Perspective to Unravel the Specific Binding Nature of 2-Methoxy Estradiol to Human β-Tubulin Isotypes. 4121-4133 - José Luis Velázquez-Libera, Julio Caballero, Jans H. Alzate-Morales, Jose Javier Ruiz-Pernía, Iñaki Tuñón:
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition. 4134-4148 - Rafael Giordano Viegas, Ingrid B. S. Martins, Vitor B. P. Leite:
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles. 4149-4157 - Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya:
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. 4158-4167 - Wen-Hao Deng, Rong-Zhen Liao:
Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. 4168-4179 - Yu Du:
Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding. 4180-4192 - Farzin Sohraby, Ariane Nunes-Alves:
Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase. 4193-4203 - Mateusz Rzycki, Dominik Drabik:
Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models. 4204-4217 - Pedro Ferreira, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria João Ramos, Pedro Alexandrino Fernandes:
DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation. 4218-4230 - Yazdan Maghsoud, Arkanil Roy, Emmett M. Leddin, G. Andrés Cisneros:
Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. 4231-4249 - Sunita Muduli, Soumyajit Karmakar, Sabyashachi Mishra:
Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling. 4250-4262 - Simona De Vita, Ester Colarusso, Maria Giovanna Chini, Giuseppe Bifulco, Gianluigi Lauro:
PharmaCore: The Automatic Generation of 3D Structure-Based Pharmacophore Models from Protein/Ligand Complexes. 4263-4276 - Jin Zhang, Xinhao Sun, Hongwei Zhao, Xu Zhou, Yiling Zhang, Feng Xie, Boyan Li, Guo Guo:
In Silico Design and Synthesis of Antifungal Peptides Guided by Quantitative Antifungal Activity. 4277-4285 - Ruslan Kotlyarov, Konstantinos Papachristos, Geoffrey P. F. Wood, Jonathan M. Goodman:
Leveraging Language Model Multitasking To Predict C-H Borylation Selectivity. 4286-4297 - Vinay Kumar, Arkaprava Banerjee, Kunal Roy:
Breaking the Barriers: Machine-Learning-Based c-RASAR Approach for Accurate Blood-Brain Barrier Permeability Prediction. 4298-4309 - Greneter Cordoves-Delgado, César R. García-Jacas:
Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning. 4310-4321 - Jujuan Zhuang, Xinru Huang, Shuhan Liu, Wanquan Gao, Rui Su, Kexin Feng:
MulTFBS: A Spatial-Temporal Network with Multichannels for Predicting Transcription Factor Binding Sites. 4322-4333 - Ning Cheng, Li Wang, Yiping Liu, Bosheng Song, Changsong Ding:
HANSynergy: Heterogeneous Graph Attention Network for Drug Synergy Prediction. 4334-4347 - Baoming Feng, Yuan-Yuan Zhang, Xiao-Chen Zhou, Jin-Long Wang, Yinfei Feng:
MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions. 4348-4358 - Yue Luo, Lei Deng:
DPMGCDA: Deciphering circRNA-Drug Sensitivity Associations with Dual Perspective Learning and Path-Masked Graph Autoencoder. 4359-4372 - Sizhe Zhang, Xuecong Tian, Chen Chen, Ying Su, Wanhua Huang, Xiaoyi Lv, Cheng Chen, Hongyi Li:
AIGO-DTI: Predicting Drug-Target Interactions Based on Improved Drug Properties Combined with Adaptive Iterative Algorithms. 4373-4384 - Jun Zhao, Qinhai Ma, Baoyue Zhang, Pengfei Guo, Zhe Wang, Yi Liu, Minsi Meng, Ailin Liu, Zifeng Yang, Guanhua Du:
Correction to "Exploration of SARS-CoV-2 3CLpro Inhibitors by Virtual Screening Methods, FRET Detection, and CPE Assay". 4385-4386
Volume 64, Number 11, 2024
- James Wellnitz, Holli-Joi Martin, Mohammad Anwar Hossain, Marielle Rath, Colton Fox, Konstantin I. Popov, Timothy M. Willson, Eugene N. Muratov, Alexander Tropsha:
STOPLIGHT: A Hit Scoring Calculator. 4387-4391 - Kha-Dinh Luong, Ambuj K. Singh:
Application of Transformers in Cheminformatics. 4392-4409 - Siyuan Liu, Qi Yang, Long Zhang, Sanzhong Luo:
Accurate Protein pKa Prediction with Physical Organic Chemistry Guided 3D Protein Representation. 4410-4418 - Qin Xie, Andrew P. Horsfield:
Coordinate-Free and Low-Order Scaling Machine Learning Model for Atomic Partial Charge Prediction for Any Size of Molecules. 4419-4425 - Arnab Jana, Sam Shepherd, Yair Litman, David M. Wilkins:
Learning Electronic Polarizations in Aqueous Systems. 4426-4435 - Floriane Eshak, Léo Pion, Pauline Scholler, Damien Nevoltris, Patrick Chames, Philippe Rondard, Jean-Philippe Pin, Francine C. Acher, Anne Goupil-Lamy:
Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques. 4436-4461 - Brunno A. Salvatti, Marcelo A. Chagas, Philipe de Oliveira Fernandes, Yan F. X. Ladeira, Aline S. Bozzi, Veronica S. Valadares, Ana Paula Valente, Amanda S. de Miranda, Willian R. Rocha, Vinicius Gonçalves Maltarollo, Adolfo H. Moraes:
Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones. 4462-4474 - Genki Kudo, Takumi Hirao, Ryunosuke Yoshino, Yasuteru Shigeta, Takatsugu Hirokawa:
Site Identification and Next Choice Protocol for Hit-to-Lead Optimization. 4475-4484 - Christian Kersten, Philippe Archambault, Luca P. Köhler:
Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. 4485-4499 - Fengjuan Huang, Jiahui Huang, Jiajia Yan, Yuying Liu, Jiangfang Lian, Qinxue Sun, Feng Ding, Yunxiang Sun:
Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin. 4500-4510 - Hyeonjun Kim, Youngshang Pak:
Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA. 4511-4517 - Hyeona Kang, Sun-Gu Lee:
Scalable Analysis of Dipole Moment Fluctuations for Characterizing Intermolecular Interactions and Structural Stability. 4518-4529 - Qian-Qian Wang, Jinshuai Song, Donghui Wei:
Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions. 4530-4541 - Nikolai V. Krivoshchapov, Michael G. Medvedev:
Accurate and Efficient Conformer Sampling of Cyclic Drug-Like Molecules with Inverse Kinematics. 4542-4552 - Christopher Vorreiter, Dina Robaa, Wolfgang Sippl:
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains. 4553-4569 - Stefano Bosio, Mattia Bernetti, Walter Rocchia, Matteo Masetti:
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. 4570-4586 - Lauri Urvas, Luca Chiesa, Guillaume Bret, Célien Jacquemard, Esther Kellenberger:
Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes. 4587-4600
Volume 64, Number 12, 2024
- Ethan Berger, Juha Niemelä, Outi Lampela, André H. Juffer, Hannu-Pekka Komsa:
Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities. 4601-4612 - Cailum M. K. Stienstra, Liam Hebert, Patrick Thomas, Alexander Haack, Jason Guo, W. Scott Hopkins:
Graphormer-IR: Graph Transformers Predict Experimental IR Spectra Using Highly Specialized Attention. 4613-4629 - Meitar Sela, Jonathan R. Church, Igor Schapiro, Dina Schneidman-Duhovny:
RhoMax: Computational Prediction of Rhodopsin Absorption Maxima Using Geometric Deep Learning. 4630-4639 - Maximilian G. Schuh, Davide Boldini, Stephan A. Sieber:
Synergizing Chemical Structures and Bioassay Descriptions for Enhanced Molecular Property Prediction in Drug Discovery. 4640-4650 - Roshni Bhatt, David Ryan Koes, Jacob D. Durrant:
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. 4651-4660 - Patrick R. Fitzgerald, Anjali Dixit, Chris Zhang, David L. Mobley, Brian M. Paegel:
Building Block-Centric Approach to DNA-Encoded Library Design. 4661-4672 - Akie Kowaguchi, Paul E. Brumby, Kenji Yasuoka:
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization. 4673-4686 - Francesco Rianjongdee, David Palmer, Stephen D. Pickett, Peter Pogány, Nicholas C. O. Tomkinson, Darren V. S. Green:
bbSelect - An Open-Source Tool for Performing a 3D Pharmacophore-Driven Diverse Selection of R-Groups. 4687-4699 - Tobias Rau, Michael Sedlmair, Andreas Köhn:
chARpack: The Chemistry Augmented Reality Package. 4700-4708 - Rutika Patel, Augustine Onyema, Phu K. Tang, Sharon M. Loverde:
Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. 4709-4726 - Patrick Kunzmann, Jan Hendrik Krumbach, Andrea Saponaro, Anna Moroni, Gerhard Thiel, Kay Hamacher:
Anisotropic Network Analysis of Open/Closed HCN4 Channel Advocates Asymmetric Subunit Cooperativity in cAMP Modulation of Gating. 4727-4738 - Xinpei Wang, Xu Chen, Zhidong Chen, Wanting Xu, Ruizhi Lai, Xiaohui Qiu, Zekai Zeng, Chenglin Wang, Zhe Wang, Junqing Wang:
Integrated Anchored Stapling and Hierarchical Dynamics: MSICDA-Driven CREBBP Bromodomain Inhibition. 4739-4758 - Felipe Bravo-Moraga, Mauricio Bedoya, Ariela Vergara Jaque, Jans H. Alzate-Morales:
Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified using Conventional and Enhanced Molecular Dynamics Simulations. 4759-4772 - Kecheng Yang, Hongmin Liu:
Mining the Dynamical Properties of Substrate and FAD Binding Pockets of LSD1: Hints for New Inhibitor Design Direction. 4773-4780 - Maria Pechlaner, Wilfred F. van Gunsteren, Lorna J. Smith, Bartosz Stankiewicz, Lukas N. Wirz, Niels Hansen:
Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach. 4781-4801 - Jesús Lucia-Tamudo, Sergio Díaz-Tendero, Juan J. Nogueira:
Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. 4802-4810 - Dongxiao Hao, Li-na Niu:
Computational Study on the Wealth Conformations of Hepatitis C Virus Envelope Glycoprotein 2 and Role of Its Glycan Coat. 4811-4821 - Muyun Lihan, Emad Tajkhorshid:
Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. 4822-4834 - Hao Guo, Zheyuan Shen, Yong-yi Yuan, Rou-fen Chen, Jing-yi Yang, Xing-chen Liu, Qing Zhang, Qian-ying Pan, Jian-jun Ding, Xin-jun He, Qing-nan Zhang, Xiaowu Dong, Ke-shu Zhou:
Discovery of a Novel and Potent LCK Inhibitor for Leukemia Treatment via Deep Learning and Molecular Docking. 4835-4849 - Martina Piga, Zoltán Varga, Adam Feher, Ferenc Papp, Eva Korpos, Kavya C. Bangera, Rok Frlan, Janez Ilas, Jaka Dernovsek, Tihomir Tomasic, Nace Zidar:
Identification of a Novel Structural Class of HV1 Inhibitors by Structure-Based Virtual Screening. 4850-4862 - Qin Zeng, Guangpeng Meng, Bingyu Zhao, Haodian Lin, Yuqing Guan, Xiaobin Qin, Yu Yuan, Yuanbo Li, Qiantao Wang:
Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor. 4863-4876 - Luosen Wang, Jie Hou, Peng Cao, Zhiying Yao, Shijun Wang, Yuying Zhang, Sheng Wang, Haoliang Yuan, Liu Liu:
Design, Synthesis, and Biological Evaluation of Chroman Derivatives as PD-1/PD-L1 Antagonists. 4877-4896 - Sita Sirisha Madugula, Pranav Pujar, Bharani Nammi, Shouyi Wang, Vindi M. Jayasinghe-Arachchige, Tyler Pham, Dominic Mashburn, Maria Artiles, Jin Liu:
Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum. 4897-4911 - Marco Giulini, Raffaele Fiorentini, Luca Tubiana, Raffaello Potestio, Roberto Menichetti:
EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations. 4912-4927 - Xiang Du, Xinliang Sun, Min Li:
Knowledge Graph Convolutional Network with Heuristic Search for Drug Repositioning. 4928-4937
Volume 64, Number 13, 2024
- Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu:
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. 4939-4940 - Sadik Bhattarai, Hilal Tayara, Kil To Chong:
Advancing Peptide-Based Cancer Therapy with AI: In-Depth Analysis of State-of-the-Art AI Models. 4941-4957 - Xuefeng Bai, Yabo Xie, Xin Zhang, Honggui Han, Jian-Rong Li:
Evaluation of Open-Source Large Language Models for Metal-Organic Frameworks Research. 4958-4965 - Yifei Yue, Saad Aldin Mohamed, Jianwen Jiang:
Classifying and Predicting the Thermal Expansion Properties of Metal-Organic Frameworks: A Data-Driven Approach. 4966-4979 - Amit Ranjan, Adam Bess, Chris Alvin, Supratik Mukhopadhyay:
MDF-DTA: A Multi-Dimensional Fusion Approach for Drug-Target Binding Affinity Prediction. 4980-4990 - Abdallah Abou Hajal, Richard A. Bryce, Boulbaba Ben Amor, Noor Atatreh, Mohammad A. Ghattas:
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter. 4991-5005 - Matthew Glace, Roudabeh S. Moazeni-Pourasil, Daniel W. Cook, Thomas D. Roper:
Iterative Regression of Corrective Baselines (IRCB): A New Model for Quantitative Spectroscopy. 5006-5015 - Nanqi Hong, Dejun Jiang, Zhe Wang, Huiyong Sun, Hao Luo, Lingjie Bao, Mingli Song, Yu Kang, Tingjun Hou:
TransfIGN: A Structure-Based Deep Learning Method for Modeling the Interaction between HLA-A*02:01 and Antigen Peptides. 5016-5027 - Jungwoo Kim, Woojae Chang, Hyunjun Ji, Insuk Joung:
Quantum-Informed Molecular Representation Learning Enhancing ADMET Property Prediction. 5028-5040 - Fatma Cankara, Simge Senyuz, Ahenk Zeynep Sayin, Attila Gürsoy, Ozlem Keskin:
DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces. 5041-5051 - Yating Lin, Jun Xu, Qiong Gu:
FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations. 5052-5062 - David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern:
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. 5063-5076 - Aditya Kulkarni, Michael Bortz, Karl-Heinz Küfer, Maximilian Kohns, Hans Hasse:
Hierarchical Multicriteria Optimization of Molecular Models of Water. 5077-5089 - Muhammad Haseeb, Yang Seon Choi, Mahesh Chandra Patra, Uisuk Jeong, Wang Hee Lee, Naila Qayyum, Hongjoon Choi, Wook Kim, Sangdun Choi:
Discovery of Novel Small Molecule Dual Inhibitor Targeting Toll-Like Receptors 7 and 9. 5090-5107 - Josh Kemppainen, Jacob R. Gissinger, S. Gowtham, Gregory M. Odegard:
LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations. 5108-5126 - Ana M. Muñoz, Víctor H. Orozco, Lina M. Hoyos, Luis F. Giraldo, Cesar A. Pérez:
Rational Design of Molecularly Imprinted Polymers for Curcuminoids Binding: Computational and Experimental Approaches for the Selection of Functional Monomers. 5127-5139 - Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos:
Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators. 5140-5150 - Zakaria L. Dahmani, Ana Ligia Scott, Catherine Vénien-Bryan, David Perahia, Mauricio G. S. Costa:
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 5151-5160 - Xin Xia, Yiping Liu, Chunhou Zheng, Xingyi Zhang, Qingwen Wu, Xin Gao, Xiangxiang Zeng, Yansen Su:
Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space. 5161-5174 - Romain Launay, Sophie-Carole Chobert, Sophie S. Abby, Fabien Pierrel, Isabelle André, Jérémy Esque:
Structural Reconstruction of E. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework. 5175-5193 - Leon Wehrhan, Bettina G. Keller:
Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin-BPTI Complex Using Random Acceleration Molecular Dynamics Simulations. 5194-5206 - Yuan-Ling Xia, Wen-Wen Du, Yong-Ping Li, Yan Tao, Zhi-Bi Zhang, Song-Ming Liu, Yun-Xin Fu, Ke-Qin Zhang, Shu-Qun Liu:
Computational Insights into SARS-CoV-2 Main Protease Mutations and Nirmatrelvir Efficacy: The Effects of P132H and P132H-A173V. 5207-5218 - Qianjun Xu, Maohua Yang, Jie Ji, Jingwei Weng, Wenning Wang, Xin Xu:
Impact of Nonnative Interactions on the Binding Kinetics of Intrinsically Disordered p53 with MDM2: Insights from All-Atom Simulation and Markov State Model Analysis. 5219-5231 - Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M. Cook, Kurt L. Krause, James Andrew McCammon:
Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. 5232-5241 - Andres S. Arango, Hyun Park, Emad Tajkhorshid:
Topological Learning Approach to Characterizing Biological Membranes. 5242-5252 - Pu Jiang, Cong Zhang, Hongshuang Wang, Penghui Li, Xiubo Du, Yibo Wang, Ekaterina Lyukmanova, Cong Lin, Xiaohui Wang:
Nicotine Enantioselectively Targets Myeloid Differentiation Protein 2 and Inhibits the Toll-like Receptor 4 Signaling. 5253-5261 - Bryan M. Delfing, Xavier E. Laracuente, William Jeffries, Xingyu Luo, Audrey Olson, Kenneth W. Foreman, Greg Petruncio, Kyung Hyeon Lee, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K. Klimov:
Competitive Binding of Viral Nuclear Localization Signal Peptide and Inhibitor Ligands to Importin-α Nuclear Transport Protein. 5262-5272 - Jingwei Gao, Cong Zhang, Hangyu Xu, Tianshu Zhang, Hongshuang Wang, Yibo Wang, Xiaohui Wang:
Dissecting the Role of the Hydroxyl Moiety at C14 in (+)-Opioid-Based TLR4 Antagonists via Wet-Lab Experiments and Molecular Dynamics Simulations. 5273-5284 - David Ricardo Figueroa Blanco, Pietro Vidossich, Marco de Vivo:
Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes. 5285-5294 - Magnus Lundborg, Christian Wennberg, Erik Lindahl, Lars Norlén:
Simulating the Skin Permeation Process of Ionizable Molecules. 5295-5302 - Xinjie Fan, Xiaohan Zhang, Jiajia Yan, Huan Xu, Wenhui Zhao, Feng Ding, Fengjuan Huang, Yunxiang Sun:
Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes. 5303-5316 - Siqi Chen, Nan Gao, Chunzhi Li, Fei Zhai, Xiwei Jiang, Peng Zhang, Jibin Guan, Kefeng Li, Rongwu Xiang, Guixia Ling:
DrugSK: A Stacked Ensemble Learning Framework for Predicting Drug Combinations of Multiple Diseases. 5317-5327 - Kriti Shukla, Kelvin Idanwekhai, Martin Naradikian, Stephanie Ting, Stephen P. Schoenberger, Elizabeth Brunk:
Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation. 5328-5343 - Merveille K. I. Eguida, Guillaume Bret, François Sindt, Fengling Li, Irene Chau, Suzanne Ackloo, Cheryl H. Arrowsmith, Albina Bolotokova, Pegah Ghiabi, Elisa Gibson, Levon Halabelian, Scott Houliston, Rachel J. Harding, Ashley Hutchinson, Peter Loppnau, Sumera Perveen, Almagul Seitova, Hong Zeng, Matthieu Schapira, Didier Rognan:
Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2. 5344-5355 - Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás:
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". 5356
Volume 64, Number 14, 2024
- Benjamin Ries, Irfan Alibay, Nithishwer Mouroug Anand, Philip C. Biggin, Aniket Magarkar:
Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery. 5357-5364 - Lewis H. Mervin, Alexey Voronov, Mikhail Kabeshov, Ola Engkvist:
QSARtuna: An Automated QSAR Modeling Platform for Molecular Property Prediction in Drug Design. 5365-5374 - Inbal Tuvi-Arad, Yaffa Shalit, Gil Alon:
CSM Software: Continuous Symmetry and Chirality Measures for Quantitative Structural Analysis. 5375-5380 - Chao Shen, Jianfei Song, Chang-Yu Hsieh, Dong-Sheng Cao, Yu Kang, Wenling Ye, Zhenxing Wu, Jike Wang, Odin Zhang, Xujun Zhang, Hao Zeng, Heng Cai, Yu Chen, Linkang Chen, Hao Luo, Xinda Zhao, Tianye Jian, Tong Chen, Dejun Jiang, Mingyang Wang, Qing Ye, Jialu Wu, Hongyan Du, Hui Shi, Yafeng Deng, Tingjun Hou:
DrugFlow: An AI-Driven One-Stop Platform for Innovative Drug Discovery. 5381-5391 - Letizia Fiorucci, Marco Schiavina, Isabella C. Felli, Roberta Pierattelli, Enrico Ravera:
Are Protein Conformational Ensembles in Agreement with Experimental Data? A Geometrical Interpretation of the Problem. 5392-5401 - Stefan Semrau:
Neural Network-Based Filter Design for Compressive Raman Classification of Cells. 5402-5412 - Haihan Liu, Baichun Hu, Peiying Chen, Xiao Wang, Hanxun Wang, Shizun Wang, Jian Wang, Bin Lin, Mao-Sheng Cheng:
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets. 5413-5426 - Chengtao Pu, Lingxi Gu, Yuxuan Hu, Weijie Han, Xiaohe Xu, Haichun Liu, Yadong Chen, Yanmin Zhang:
Prediction of Human Liver Microsome Clearance with Chirality-Focused Graph Neural Networks. 5427-5438 - Zachary J. Gale-Day, Laura Shub, Kangway V. Chuang, Michael J. Keiser:
Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks. 5439-5450 - Gökhan Tahil, Fabien Delorme, Daniel Le Berre, Éric Monflier, Adlane Sayede, Sébastien Tilloy:
Stereoisomers Are Not Machine Learning's Best Friends. 5451-5469 - Junren Li, Kangjie Lin, Jianfeng Pei, Luhua Lai:
Challenging Complexity with Simplicity: Rethinking the Role of Single-Step Models in Computer-Aided Synthesis Planning. 5470-5479 - Hongle An, Xuyang Liu, Wensheng Cai, Xueguang Shao:
AttenGpKa: A Universal Predictor of Solvation Acidity Using Graph Neural Network and Molecular Topology. 5480-5491 - Peter Eckmann, Jake Anderson, Rose Yu, Michael K. Gilson:
Ligand-Based Compound Activity Prediction via Few-Shot Learning. 5492-5499 - Shuyu Wang, Hongxing Yue, Xiaoming Yuan:
Accelerating Polymer Discovery with Uncertainty-Guided PGCNN: Explainable AI for Predicting Properties and Mechanistic Insights. 5500-5509 - Manuel Carrer, Henrique M. Cezar, Sigbjørn Løland Bore, Morten Ledum, Michele Cascella:
Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics. 5510-5520 - Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay:
OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. 5521-5534 - Fangting Li, Kun Lv, Xiaohua Liu, Yuqiao Zhou, Kai Liu:
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models. 5535-5546 - Linh Ho Manh, Victoria C. P. Chen, Jay M. Rosenberger, Shouyi Wang, Yujing Yang, Kevin A. Schug:
Prediction of Vacuum Ultraviolet/Ultraviolet Gas-Phase Absorption Spectra Using Molecular Feature Representations and Machine Learning. 5547-5556 - Itsuki Maeda, Shunsuke Tamura, Yoshihiro Ogura, Takayuki Serizawa, Takashi Shimada, Ryo Kunimoto, Tomoyuki Miyao:
Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test. 5557-5569 - Ciceron Ayala-Orzoco, Hamid Teimouri, Angela Medvedeva, Bowen Li, Alex Lathem, Gang Li, Anatoly B. Kolomeisky, James M. Tour:
Chemoinformatics Insights on Molecular Jackhammers and Cancer Cells. 5570-5579 - Ranabir Majumder, Shreya Banerjee, Sayan Paul, Saugat Mondal, Madhurima Mandal, Priya Ghosh, Debjit Maity, Anakuthil Anoop, N. D. Pradeep Singh, Mahitosh Mandal:
Riboflavin-Induced DNA Damage and Anticancer Activity in Breast Cancer Cells under Visible Light: A TD-DFT and In Vitro Study. 5580-5589 - Debashree Chakraborty, Omkar Singh, Divya Parameswaran:
Study of Correlated Motions to Detect the Conformational Transitions of the Intrinsically Disordered Sheep Prion Peptide. 5590-5603 - Vicente Martí-Centelles, Tomasz K. Piskorz, Fernanda Duarte:
CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages. 5604-5616 - Tao Liu, Lena Simine:
DeltaGzip: Computing Biopolymer-Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression. 5617-5623 - Zijing Tian, Yan Dai, Feng Hu, Zihao Shen, Hongling Xu, Hongwen Zhang, Jinhang Xu, Yuting Hu, Yanyan Diao, Honglin Li:
Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds. 5624-5633 - Emanuele Falbo, Antonio Lavecchia:
HessFit: A Toolkit to Derive Automated Force Fields from Quantum Mechanical Information. 5634-5645 - Shuo Liu, Jialiang Yu, Ningxi Ni, Zidong Wang, Mengyun Chen, Yuquan Li, Chen Xu, Yahao Ding, Jun Zhang, Xiaojun Yao, Huanxiang Liu:
Versatile Framework for Drug-Target Interaction Prediction by Considering Domain-Specific Features. 5646-5656 - Monica P. Barron, Jonah Z. Vilseck:
A λ-Dynamics Investigation of Insulin Wakayama and Other A3 Variant Binding Affinities to the Insulin Receptor. 5657-5670 - Han Zhang, Wonpil Im:
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. 5671-5679 - Zhiyu Zhao, Emad Tajkhorshid:
GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. 5680-5690 - Jakob Liu, Andreas Fischer, Monika Cserjan-Puschmann, Nico Lingg, Chris Oostenbrink:
Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation. 5691-5700 - Lisa Lombardo, Salvatore Mirabile, Rosaria Gitto, Giuseppe Cosentino, Stefano Alcaro, Maria Dichiara, Agostino Marrazzo, Emanuele Amata, Francesco Ortuso, Laura De Luca:
Exploring Structural Requirements for Sigma-1 Receptor Linear Ligands: Experimental and Computational Approaches. 5701-5711 - Nanako Inoue, Tomokazu Shibata, Yusuke Tanaka, Hiromu Taguchi, Ryusuke Sawada, Kenshin Goto, Shogo Momokita, Morihiro Aoyagi, Takashi Hirao, Yoshihiro Yamanishi:
Revealing Comprehensive Food Functionalities and Mechanisms of Action through Machine Learning. 5712-5724 - Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee:
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. 5725-5736
Volume 64, Number 15, 2024
- Ganna Gryn'ova, Tristan Bereau, Carolin Müller, Pascal Friederich, Rebecca C. Wade, Ariane Nunes-Alves, Thereza A. Soares, Kenneth M. Merz Jr.:
EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. 5737-5738 - Peter V. Coveney, Roger R. Highfield:
Artificial Intelligence Must Be Made More Scientific. 5739-5741 - Boris Gomaz, Alessandro Pandini, Aleksandra Marsavelski, Zoran Stefanic:
MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams. 5742-5748 - Darian T. Yang, Lillian T. Chong:
WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data. 5749-5755 - Philipp Renz, Sohvi Luukkonen, Günter Klambauer:
Diverse Hits in De Novo Molecule Design: Diversity-Based Comparison of Goal-Directed Generators. 5756-5761 - Shokirbek Shermukhamedov, Dilorom Mamurjonova, Thana Maihom, Michael Probst:
Structure to Property: Chemical Element Embeddings for Predicting Electronic Properties of Crystals. 5762-5770 - Puck van Gerwen, Ksenia R. Briling, Charlotte Bunne, Vignesh Ram Somnath, Rubén Laplaza, Andreas Krause, Clémence Corminboeuf:
3DReact: Geometric Deep Learning for Chemical Reactions. 5771-5785 - Oliver Snow, Amirreza Kazemi, Forum Bhanshali, Alyas Nasiri, Annett Rozek, Martin Ester:
Identifying Synergistic Components of Botanical Fungicide Formulations Using Interpretable Graph Neural Networks. 5786-5795 - Olaf Wiest, Christoph Alexander Bauer, Paul Helquist, Per-Ola Norrby, Samuel Genheden:
Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions. 5796-5805 - Richard Overstreet, Ethan King, Grady Clopton, Julia Nguyen, Danielle Ciesielski:
QC-GN2oMS2: a Graph Neural Net for High Resolution Mass Spectra Prediction. 5806-5816 - Alvaro Prat, Hisham Abdel-Aty, Orestis Bastas, Gintautas Kamuntavicius, Tanya Paquet, Povilas Norvaisas, Piero Gasparotto, Roy Tal:
HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discovery. 5817-5831 - Gayane Chilingaryan, Hovhannes Tamoyan, Ani Tevosyan, Nelly Babayan, Karen Hambardzumyan, Zaven Navoyan, Armen Aghajanyan, Hrant Khachatrian, Lusine Khondkaryan:
BartSmiles: Generative Masked Language Models for Molecular Representations. 5832-5843 - Yuki Matsukiyo, Atsushi Tengeiji, Chen Li, Yoshihiro Yamanishi:
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design. 5844-5852 - Qingtian Zhang, Dangxin Mao, Yusong Tu, Yuan-Yan Wu:
A New Fingerprint and Graph Hybrid Neural Network for Predicting Molecular Properties. 5853-5866 - Geng Chen, Yiyang Qin, Rong Sheng:
Integrating Prior Chemical Knowledge into the Graph Transformer Network to Predict the Stability Constants of Chelating Agents and Metal Ions. 5867-5877 - Luisa Vollmer, Sophie Fellenz, Fabian Jirasek, Heike Leitte, Hans Hasse:
KnowTD─An Actionable Knowledge Representation System for Thermodynamics. 5878-5887 - Abdulelah S. Alshehri, Kai A. Horstmann, Fengqi You:
Versatile Deep Learning Pipeline for Transferable Chemical Data Extraction. 5888-5899 - Albert Bou, Morgan Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis:
ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. 5900-5911 - Gen Li, Ning Zhang, Xiaowen Dai, Long Fan:
EnzyACT: A Novel Deep Learning Method to Predict the Impacts of Single and Multiple Mutations on Enzyme Activity. 5912-5921 - Matthew A. Dorsey, Kelvin Dsouza, Dhruv Ranganath, Joshua S. Harris, Thomas R. Lane, Fabio Urbina, Sean Ekins:
Near-Term Quantum Classification Algorithms Applied to Antimalarial Drug Discovery. 5922-5930 - Xiaochao Wang, Wanli Zhang, Wenxu Zhang:
Dielectric Ceramics Database Automatically Constructed by Data Mining in the Literature. 5931-5943 - Joel Wahl:
PheSA: An Open-Source Tool for Pharmacophore-Enhanced Shape Alignment. 5944-5953 - Kavinda Kashi Juliyan Gunasinghe, Irine Runnie Henry Ginjom, Hwang Siaw San, Taufiq Rahman, Xavier Chee Wezen:
Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors? 5954-5963 - Rakesh Kumar Roy, Abhishek Bera, Niladri Patra:
Insights into Allosteric Inhibition of the AcrB Efflux Pump: Role of Distinct Binding Pockets, Protomer Preferences, and Crosstalk Disruption. 5964-5976 - Antonio M. Bosch, Horacio V. Guzman, Rubén Pérez:
Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. 5977-5990 - Bongkochawan Pakamwong, Paptawan Thongdee, Bundit Kamsri, Naruedon Phusi, Somjintana Taveepanich, Kampanart Chayajarus, Pharit Kamsri, Auradee Punkvang, Supa Hannongbua, Jidapa Sangswan, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Jiraporn Leanpolchareanchai, James Spencer, Adrian J. Mulholland, Pornpan Pungpo:
Ligand-Based Virtual Screening for Discovery of Indole Derivatives as Potent DNA Gyrase ATPase Inhibitors Active against Mycobacterium tuberculosis and Hit Validation by Biological Assays. 5991-6002 - Daichi Hayakawa, Yurie Watanabe, Hiroaki Gouda:
Molecular Interaction Fields Describing Halogen Bond Formable Areas on Protein Surfaces. 6003-6013 - Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix Jurgal Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky:
Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. 6014-6025 - Daniel Becker, Prasad V. Bharatam, Holger Gohlke:
Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6. 6026-6040 - Jordan A. P. McIvor, Danaé S. Larsen, Davide Mercadante:
Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. 6041-6052 - Yiling Liu, Jundong Tan, Shiliang Hu, Muzammal Hussain, Chang Qiao, Yaoquan Tu, Xiaoyun Lu, Yang Zhou:
Dynamics Playing a Key Role in the Covalent Binding of Inhibitors to Focal Adhesion Kinase. 6053-6061 - Yasir Mamun, Yuk-Ching Tse-Dinh, Prem Chapagain:
Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations. 6062-6071 - Peng Gao, Mitali Tambe, Catherine Z. Chen, Wenwei Huang, Gregory J. Tawa, Tal Hirschhorn, Brent R. Stockwell, Wei Zheng, Min Shen:
Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening. 6072-6080 - Olympia-Dialekti Vouzina, Alexandros Tafanidis, Nicholas M. Glykos:
The Curious Case of A31P, a Topology-Switching Mutant of the Repressor of Primer Protein: A Molecular Dynamics Study of Its Folding and Misfolding. 6081-6091 - Jason T. Linzer, Ethan Aminov, Aalim S. Abdullah, Colleen E. Kirkup, Rebeca I. Diaz Ventura, Vinay R. Bijoor, Jiyun Jung, Sophie Huang, Chi Gee Tse, Emily Álvarez Toucet, Hugo P. Onghai, Arghya P. Ghosh, Alex C. Grodzki, Emilee R. Haines, Aditya S. Iyer, Mark K. Khalil, Alexander P. Leong, Michael A. Neuhaus, Joseph Park, Asir Shahid, Matthew Xie, Jan M. Ziembicki, Carlos Simmerling, Maria C. Nagan:
Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment. 6092-6104 - Oskar Svensson, Michael J. Bakker, Marie Skepö:
Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins. 6105-6114 - Gabriel F. Martins, Nuno Galamba:
Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study. 6115-6131 - Ying-Chu Hsu, Ching-Hui Liu, Yi-Chen Wu, Shu-Jung Lai, Chi-Jan Lin, Tien-Sheng Tseng:
Combatting Antibiotic-Resistant Staphylococcus aureus: Discovery of TST1N-224, a Potent Inhibitor Targeting Response Regulator VraRC, through Pharmacophore-Based Screening and Molecular Characterizations. 6132-6146 - Xuedong Li, Chengzhao Wang, Xu Chai, Xingang Liu, Kening Qiao, Yan Fu, Yanzhao Jin, Qingzhong Jia, Feng Zhu, Yang Zhang:
Discovery of Potent Selective HDAC6 Inhibitors with 5-Phenyl-1H-indole Fragment: Virtual Screening, Rational Design, and Biological Evaluation. 6147-6161 - Evianne Rovers, Matthieu Schapira:
Benchmarking Methods for PROTAC Ternary Complex Structure Prediction. 6162-6173 - Hong-Hin Cheong, Weimin Zuo, Jiarui Chen, Chon-Wai Un, Yain-Whar Si, Koon Ho Wong, Hang Fai Kwok, Shirley W. I. Siu:
Identification of Anticancer Peptides from the Genome of Candida albicans: in Silico Screening, in Vitro and in Vivo Validations. 6174-6189 - Gregory Mathez, Andrea Brancale, Valeria Cagno:
Novel Inhibitors of SARS-CoV-2 RNA Identified through Virtual Screening. 6190-6196 - Fangrui Hu, Fubin Chang, Lianci Tao, Xiaohan Sun, Lamei Liu, Yingchun Zhao, Zhongjie Han, Chunhua Li:
Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model. 6197-6204 - Zhihao Wang, Fan Zhou, Zechen Wang, Qiuyue Hu, Yong-Qiang Li, Sheng Wang, Yanjie Wei, Liangzhen Zheng, Weifeng Li, Xiangda Peng:
Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling. 6205-6215 - Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu:
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. 6216-6229 - Yanxi Zhao, Junru Jin, Wenjia Gao, Jianbo Qiao, Leyi Wei:
Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction. 6230-6240
Volume 64, Number 16, 2024
- Issue Publication Information.
- Issue Editorial Masthead.
- Sergey Gorelov, Anatoly Titov, Olga Tolicheva, Andrey Konevega, Alexey Shvetsov:
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation. 6241-6246 - Gregory A. Landrum, Jessica Braun, Paul Katzberger, Marc Lehner, Sereina Riniker:
lwreg: A Lightweight System for Chemical Registration and Data Storage. 6247-6252 - Yue Qian, Le Li, Yanning Liu, Piaopiao Zhao, Zhuwei Xie:
Breaking the Gender Imbalance: Female Presence in the Computational Chemistry Group at Viva Biotech. 6253-6258 - Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer:
Transformers for Molecular Property Prediction: Lessons Learned from the Past Five Years. 6259-6280 - Wilfred F. van Gunsteren, Chris Oostenbrink:
Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. 6281-6304 - Cheng Wang, Chuang Yuan, Yahui Wang, Yuying Shi, Tao Zhang, Gary J. Patti:
Predicting Collision Cross-Section Values for Small Molecules through Chemical Class-Based Multimodal Graph Attention Network. 6305-6315 - Hengyu Qin, Xiumin Shi, Han Zhou:
scSwinFormer: A Transformer-Based Cell-Type Annotation Method for scRNA-Seq Data Using Smooth Gene Embedding and Global Features. 6316-6323 - Matthew Adrian, Yunsie Chung, Alan C. Cheng:
Denoising Drug Discovery Data for Improved Absorption, Distribution, Metabolism, Excretion, and Toxicity Property Prediction. 6324-6337 - Yang Tan, Mingchen Li, Bingxin Zhou, Bozitao Zhong, Lirong Zheng, Pan Tan, Ziyi Zhou, Huiqun Yu, Guisheng Fan, Liang Hong:
Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models. 6338-6349 - Alexander-Maurice Illig, Niklas E. Siedhoff, Mehdi D. Davari, Ulrich Schwaneberg:
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort. 6350-6360 - Xu Li, Haoliang Zhong, Haoyu Yang, Lin Li, Qingji Wang:
High-Throughput Screening and Prediction of Nucleophilicity of Amines Using Machine Learning and DFT Calculations. 6361-6368 - Hong Sun, Sébastien Hamel, Tim Hsu, Babak Sadigh, Vincenzo Lordi, Fei Zhou:
Ice Phase Classification Made Easy with Score-Based Denoising. 6369-6376 - Esther Heid, Johannes Schörghuber, Ralf Wanzenböck, Georg K. H. Madsen:
Spatially Resolved Uncertainties for Machine Learning Potentials. 6377-6387 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Machine-Learning Prediction of Curie Temperature from Chemical Compositions of Ferromagnetic Materials. 6388-6409 - Issar Arab, Kris Laukens, Wout Bittremieux:
Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set. 6410-6420 - Aamir Mehmood, Aman Chandra Kaushik, Dong-Qing Wei:
DDSBC: A Stacking Ensemble Classifier-Based Approach for Breast Cancer Drug-Pair Cell Synergy Prediction. 6421-6431 - Qirui Deng, Zhe Wang, Sutong Xiang, Qinghua Wang, Yifei Liu, Tingjun Hou, Huiyong Sun:
RLpMIEC: High-Affinity Peptide Generation Targeting Major Histocompatibility Complex-I Guided and Interpreted by Interaction Spectrum-Navigated Reinforcement Learning. 6432-6449 - Jesse A. Weller, Remo Rohs:
Structure-Based Drug Design with a Deep Hierarchical Generative Model. 6450-6463 - Nathan J. Rebello, Akash Arora, Hidenobu Mochigase, Tzyy-Shyang Lin, Jiale Shi, Debra J. Audus, Eric S. Muckley, Ardiana Osmani, Bradley D. Olsen:
The Block Copolymer Phase Behavior Database. 6464-6476 - Yiru Huang, Lei Zhang, Hangyuan Deng, Junfei Mao:
NJmat: Data-Driven Machine Learning Interface to Accelerate Material Design. 6477-6491 - Deedar Nabi, Aaron J. Beck, Eric P. Achterberg:
Assessing Aquatic Baseline Toxicity of Plastic-Associated Chemicals: Development and Validation of the Target Plastic Model. 6492-6505 - Youyou Yang, Wenli Gan, Lei Lin, Long Wang, Jianming Wu, Jiesi Luo:
Identification of Active Molecules against Thrombocytopenia through Machine Learning. 6506-6520 - Katarzyna Bednarska-Szczepaniak, Krzysztof Halagan, Marzena Szwed, Ewelina Przelazly, Zbigniew J. Lesnikowski:
Quantum Chemical and Biological Insights into Redox Activity of Metallacarborane Complexes in Cancer Cells. 6521-6541 - Michael J. Bakker, Amina Gaffour, Martin Juhás, Vojtech Zapletal, Jakub Stosek, Lars A. Bratholm, Jana Pavlíková Precechtelová:
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering. 6542-6556 - Olivér Pavela, Tünde Juhász, Liliána Tóth, András Czajlik, Gyula Batta, László Galgóczy, Tamás Beke-Somfai:
Mapping of the Lipid-Binding Regions of the Antifungal Protein NFAP2 by Exploiting Model Membranes. 6557-6569 - Jules Marien, Chantal Prévost, Sophie Sacquin-Mora:
nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat. 6570-6582 - Viktor Szél, Balázs Zoltán Zsidó, Csaba Hetényi:
Enthalpic Classification of Water Molecules in Target-Ligand Binding. 6583-6595 - Shudong Wang, Hengxiao Li, Yahui Liu, Shanchen Pang, Sibo Qiao, Jionglong Su, Shaoqiang Wang, Yulin Zhang:
Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells. 6596-6609 - Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Ribosome Tunnel Environment Drives the Formation of α-Helix during Cotranslational Folding. 6610-6622 - Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky:
Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. 6623-6635 - Maximilian Beckers, Finton Sirockin, Nikolas Fechner, Nikolaus Stiefl:
Balancing Molecular Size, Activity, Permeability, and Other Properties: Drug Candidates in the Context of Their Chemical Structure Optimization. 6636-6647 - Xiaojun Fu, Changyuan Ren, Kaining Dai, Ming Ren, Changxiang Yan:
Epithelial-Mesenchymal Transition Related Score Functions as a Predictive Tool for Immunotherapy and Candidate Drugs in Glioma. 6648-6661 - Ping Xuan, Wei Wang, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Tiangang Zhang:
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction. 6662-6675 - Junjie Wee, Guo-Wei Wei:
Evaluation of AlphaFold 3's Protein-Protein Complexes for Predicting Binding Free Energy Changes upon Mutation. 6676-6683 - Lihong Peng, Xin Liu, Min Chen, Wen Liao, Jiale Mao, Liqian Zhou:
MGNDTI: A Drug-Target Interaction Prediction Framework Based on Multimodal Representation Learning and the Gating Mechanism. 6684-6698 - Yun Zuo, Bangyi Zhang, Yinkang Dong, Wenying He, Yue Bi, Xiangrong Liu, Xiangxiang Zeng, Zhaohong Deng:
Glypred: Lysine Glycation Site Prediction via CCU-LightGBM-BiLSTM Framework with Multi-Head Attention Mechanism. 6699-6711 - Jingpu Zhang, Hao Lu, Ying Jiang, Yuanyuan Ma, Lei Deng:
ncRNA Coding Potential Prediction Using BiLSTM and Transformer Encoder-Based Model. 6712-6722
Volume 64, Number 17, 2024
- Frazier N. Baker, Ziqi Chen, Daniel Adu-Ampratwum, Xia Ning:
RLSynC: Offline-Online Reinforcement Learning for Synthon Completion. 6723-6735 - Liping Sun, Jili Hu, Yinfeng Yang, Yongkang Wang, Zijian Wang, Yong Gao, Yiqi Nie, Can Liu, Hongxing Kan:
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities. 6736-6744 - Xuezhi Xie, Pedro A. Valiente, Jin Sub Lee, Jisun Kim, Philip M. Kim:
Antibody-SGM, a Score-Based Generative Model for Antibody Heavy-Chain Design. 6745-6757 - R. Beccaria, A. Lazzeri, Guido Tiana:
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure. 6758-6767 - Yuchuan Zheng, Qixiu Li, Maria I. Freiberger, Haoyu Song, Guorong Hu, Moxin Zhang, Ruo-Xu Gu, Jingyuan Li:
Predicting the Dynamic Interaction of Intrinsically Disordered Proteins. 6768-6777 - Cristian Orgaz, Andrés Sánchez-Ruiz, Gonzalo Colmenarejo:
Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites. 6778-6798 - Ayesh Madushanka, Eli J. Laird, Corey Clark, Elfi Kraka:
SmartCADD: AI-QM Empowered Drug Discovery Platform with Explainability. 6799-6813 - Changrui Xing, Guanglei Li, Xin Zheng, Peng Li, Jian Yuan, Wenjing Yan:
Characterization of a Novel Monoclonal Antibody with High Affinity and Specificity against Aflatoxins: A Discovery from Rosetta Antibody-Ligand Computational Simulation. 6814-6826 - Sara G. F. Ferreira, Manoj K. Sriramoju, Shang-Te Danny Hsu, Patrícia F. N. Faísca, Miguel Machuqueiro:
Is There a Functional Role for the Knotted Topology in Protein UCH-L1? 6827-6837 - Zanxia Cao, Zhihong Shi, Mingqiong Tong, Dongying Yang, Lei Liu:
Synergistic Antimicrobial Mechanism of the Ultrashort Antimicrobial Peptide R3W4V with a Tadpole-like Conformation. 6838-6849 - Carlos A. V. Barreto, João N. M. Vitorino, Pedro B. P. S. Reis, Miguel Machuqueiro, Irina S. Moreira:
pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation. 6850-6856 - Haochen Xu, Zhonghuai Hou, Rongbin Zhou, Jie-Lou Liao:
Rotation and Self-Assembly Driving NLRP3 Activation. 6857-6865 - Carlo Bigiotti, Elisa Bianconi, Luana Ruta, Silvia Grottelli, Alice Coletti, Mirco Dindo, Andrea Carotti, Barbara Cellini, Antonio Macchiarulo:
Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH-1. 6866-6879 - Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao, Guodong Hu:
Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning. 6880-6898 - Lingling Wang, Shu Li, Sutong Xiang, Huanxiang Liu, Huiyong Sun:
Elucidating the Selective Mechanism of Drugs Targeting Cyclin-Dependent Kinases with Integrated MetaD-US Simulation. 6899-6911 - Vishva Saravanan R, Soham Choudhuri, Bhaswar Ghosh:
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation. 6912-6925 - Eleftherios Christofi, Petra Bacová, Vagelis Harmandaris:
Correction to "Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers". 6926
Volume 64, Number 18, 2024
- Hirotomo Moriwaki, Yusuke Kawashima, Chiduru Watanabe, Kikuko Kamisaka, Yoshio Okiyama, Kaori Fukuzawa, Teruki Honma:
FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses. 6927-6937 - Gwenn Guichaoua, Philippe Pinel, Brice Hoffmann, Chloé-Agathe Azencott, Véronique Stoven:
Drug-Target Interactions Prediction at Scale: The Komet Algorithm with the LCIdb Dataset. 6938-6956 - Thanh-Hoang Nguyen-Vo, Trang T. T. Do, Binh P. Nguyen:
Multitask Learning on Graph Convolutional Residual Neural Networks for Screening of Multitarget Anticancer Compounds. 6957-6968 - Mami Ozawa, Shogo Nakamura, Nobuaki Yasuo, Masakazu Sekijima:
IEV2Mol: Molecular Generative Model Considering Protein-Ligand Interaction Energy Vectors. 6969-6978 - Jiaming Gao, Haoquan Liu, Chen Zhuo, Chengwei Zeng, Yunjie Zhao:
Predicting Small Molecule Binding Nucleotides in RNA Structures Using RNA Surface Topography. 6979-6992 - Andrew J. Whitehouse, Melchor Sanchez-Martinez, Seyedeh Maryam Salehi, Natalja Kurbatova, Euan Dean:
Open-Source Approach to GPU-Accelerated Substructure Search. 6993-7006 - Zihui Huang, Xinyi Li, Andi Li, Yuhang Yang, Liqiang He, Zhiwen Zhang, Siwei Wu, Yang Wang, Shuting Cai, Yan He, Xujie Liu:
MPNTEXT: An Interactive Platform for Automatically Extracting Metal-Polyphenol Networks and Their Applications from Scientific Literature. 7007-7016 - Francesco Cappelluti, Lorenzo Gontrani, Alessandro Mariani, Simone Galliano, Marilena Carbone, Matteo Bonomo:
Voronoi Tessellation as a Tool for Predicting the Formation of Deep Eutectic Solvents. 7017-7026 - Goran Giudetti, Madhubani Mukherjee, Samprita Nandi, Sraddha Agrawal, Oleg V. Prezhdo, Aiichiro Nakano:
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach. 7027-7034 - Tatiana I. Mulashkina, Anna M. Kulakova, Maria G. Khrenova:
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study. 7035-7045 - Hsu-Chun Tsai, James Xu, Zhenyu Guo, Yinhui Yi, Chuan Tian, Xinyu Que, Timothy J. Giese, Tai-Sung Lee, Darrin M. York, Abir Ganguly, Albert C. Pan:
Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach. 7046-7055 - Minos-Timotheos Matsoukas, Tarryn Radomsky, Vasilis Panagiotopoulos, Robin du Preez, Michail Papadourakis, Konstantinos Tsianakas, Robert P. Millar, Ross C. Anderson, Georgios A Spyroulias, Claire L. Newton:
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR). 7056-7067 - Koichi Handa, Shunta Sasaki, Satoshi Asano, Michiharu Kageyama, Takeshi Iijima, Andreas Bender:
Prediction of Inhibitory Activity against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models. 7068-7076 - Siyoung Kim:
All-Atom Membrane Builder via Multiscale Simulation. 7077-7085 - Debjyoti Bhattacharya, Harrison J. Cassady, Michael A. Hickner, Wesley F. Reinhart:
Large Language Models as Molecular Design Engines. 7086-7096 - Milo Roucairol, Alexios Georgiou, Tristan Cazenave, Filippo Prischi, Olivier E. Pardo:
DrugSynthMC: An Atom-Based Generation of Drug-like Molecules with Monte Carlo Search. 7097-7107 - Pengbo Song, Qiaojing Huang, Wenyu Li, Maodong Li, Zhirong Liu:
Decomposition of Forces in Protein: Methodology and General Properties. 7108-7121 - Miguel Riopedre-Fernandez, Vojtech Kostal, Tomás Martínek, Hector Martinez-Seara, Denys Biriukov:
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions. 7122-7134 - Reyes Núñez-Franco, M. Milagros Muriel-Olaya, Gonzalo Jiménez-Osés, Francesca Peccati:
AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants. 7135-7140 - Francesco Coppola, Roya Jafari, Katherine D. McReynolds, Petr Král:
Sulfoglycodendron Antivirals with Scalable Architectures and Activities. 7141-7151 - Yunyuan Huang, Xin Chen, Jin Yang, Yue Yao, Manjiong Wang, Taotao Lu, Xiao Li, Jiqun Wang, Sicong Qiao, Donglei Shi, Xiaokang Li, Jian Li, Yixiang Xu:
Novel Combination Therapy for Heart Failure: Trimebutine-Methoxsalen Identified through Synergistic Network Virtual Screening and Experimental Validation. 7152-7162 - Chang-Qing Yu, Xin-Fei Wang, Li-Ping Li, Zhu-Hong You, Zhong-Hao Ren, Peng Chu, Feng Guo, Zhen-Yu Wang:
RBNE-CMI: An Efficient Method for Predicting circRNA-miRNA Interactions via Multiattribute Incomplete Heterogeneous Network Embedding. 7163-7172
Volume 64, Number 19, 2024
- George Rodriguez:
Misunderstandings Regarding Sampling and the Role of Statistics in AI. 7173-7175 - Yi He, Shuang Wang, Shuai Zeng, Jingxuan Zhu, Dong Xu, Weiwei Han, Juexin Wang:
NRIMD, a Web Server for Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation. 7176-7183 - Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation. 7184-7188 - Chuanghui Wang, Yunqing Yang, Jinshuai Song, Xiaofei Nan:
Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry. 7189-7213 - Runtong Qian, Jing Xue, You Xu, Jing Huang:
Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery. 7214-7237 - Amira Alakhdar, Barnabás Póczos, Newell Washburn:
Diffusion Models in De Novo Drug Design. 7238-7256 - Jonah Poort, Milad Golkaram, Pieter Janssen, Jan Harm Urbanus:
Prediction of Acrylonitrile-Butadiene-Styrene Mechanical Properties through Compressed-Sensing Techniques. 7257-7272 - Wei Ma, Jiaqi Hu, Zhuangzhi Chen, Yaoqin Ai, Yihang Zhang, Keke Dong, Xiangfei Meng, Liu Liu:
The Development and Application of KinomePro-DL: A Deep Learning Based Online Small Molecule Kinome Selectivity Profiling Prediction Platform. 7273-7290 - Takamasa Suzuki, Dian Ma, Nobuaki Yasuo, Masakazu Sekijima:
Mothra: Multiobjective de novo Molecular Generation Using Monte Carlo Tree Search. 7291-7302 - Matthias Welsch, Steffen Hirte, Johannes Kirchmair:
Deciphering Molecular Embeddings with Centered Kernel Alignment. 7303-7312 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Predictive Modeling of High-Entropy Alloys and Amorphous Metallic Alloys Using Machine Learning. 7313-7336 - Jian Gao, Zheyuan Shen, Yan Lu, Liteng Shen, Binbin Zhou, Donghang Xu, Haibin Dai, Lei Xu, Jinxin Che, Xiaowu Dong:
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction. 7337-7348 - Son Gyo Jung, Guwon Jung, Jacqueline M. Cole:
Machine-Learning Predictions of Critical Temperatures from Chemical Compositions of Superconductors. 7349-7375 - Haowei Feng, Hua Tian:
Improving Crystal Property Prediction from a Multiplex Graph Perspective. 7376-7385 - Chen Zhuo, Jiaming Gao, Anbang Li, Xuefeng Liu, Yunjie Zhao:
A Machine Learning Method for RNA-Small Molecule Binding Preference Prediction. 7386-7397 - Brendan W. Hall, Michael J. Keiser:
Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds. 7398-7408 - Devendra K. Dhaked, Marc C. Nicklaus:
Tautomeric Conflicts in Forty Small-Molecule Databases. 7409-7421 - He Liu, Chao Shen, Haonan Li, Tingjun Hou, Yongliang Yang:
Discovery of Potent Covalent CRM1 Inhibitors Via a Customized Structure-Based Virtual Screening Pipeline and Bioassays. 7422-7431 - Jinyoung Jeong, Taehyun Park, Junho Song, Seungpyo Kang, Joonghee Won, Jungim Han, Kyoungmin Min:
Integrating Data Mining and Natural Language Processing to Construct a Melting Point Database for Organometallic Compounds. 7432-7446 - Priyanka Kumari, Madureira Sanches Ribeiro Guilherme, Pratyush Choudhary, Thomas Van Laethem, Marianne Fillet, Phillipe Hubert, Pierre Yves Sacre, Cedric Hubert:
Transfer Learning Approach to Multitarget QSRR Modeling in RPLC. 7447-7456 - Jesi Lee, Dean J. Tantillo, Lee-Ping Wang, Oliver Fiehn:
Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling. 7457-7469 - Jesi Lee, Dean J. Tantillo, Lee-Ping Wang, Oliver Fiehn:
Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics. 7470-7487 - Julian M. Ivanov, Rumiana Tenchov, Krittika Ralhan, Kavita A. Iyer, Shivangi Agarwal, Qiongqiong Zhou:
In Silico Insights: QSAR Modeling of TBK1 Kinase Inhibitors for Enhanced Drug Discovery. 7488-7502 - Xiu Li, Yuan He, Yuxuan Wang, Kaidong Lin, Xubo Lin:
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation. 7503-7512 - Pieter H. Bos, Fabio Ranalli, Emelie Flood, Shawn Watts, Daigo Inoyama, Jennifer L. Knight, Anthony J. Clark, Andrew Placzeck, Jiashi Wang, Aleksey I. Gerasyuto, Sarah Silvergleid, Wu Yin, Shaoxian Sun, Robert Abel, Sathesh Bhat:
AutoDesigner - Core Design, a De Novo Design Algorithm for Chemical Scaffolds: Application to the Design and Synthesis of Novel Selective Wee1 Inhibitors. 7513-7524 - Ian Rouse, David Power, Julia Subbotina, Vladimir Lobaskin:
NPCoronaPredict: A Computational Pipeline for the Prediction of the Nanoparticle-Biomolecule Corona. 7525-7543 - Anna Jäckering, Marc van der Kamp, Birgit Strodel, Kirill Zinovjev:
Influence of Wobbling Tryptophan and Mutations on PET Degradation Explored by QM/MM Free Energy Calculations. 7544-7554 - Guodong Hu, Xue Yu, Zhaojun Li:
Unveiling Putative Excited State and Transmission of Binding Information in the Fluoride Riboswitch. 7555-7564 - Sriram Srinivasa Raghavan, Osamu Miyashita:
ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering. 7565-7575 - Shiqinrui Xu, Chengze Huo, Xiakun Chu:
Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases. 7576-7589 - Huayuan Tang, Yunxiang Sun, Lei Wang, Pu Chun Ke, Feng Ding:
Uncovering Intermolecular Interactions Driving the Liquid-Liquid Phase Separation of the TDP-43 Low-Complexity Domain via Atomistic Dimerization Simulations. 7590-7601 - Vladimír Sládek, Polina V. Artiushenko, Dmitri G. Fedorov:
Effect of Direct and Water-Mediated Interactions on the Identification of Hotspots in Biomolecular Complexes with Multiple Subsystems. 7602-7615 - Erik B. Nordquist, Zhiguang Jia, Jianhan Chen:
Small Molecule NS11021 Promotes BK Channel Activation by Increasing Inner Pore Hydration. 7616-7625 - Zsolt Fazekas, Dóra Nagy-Fazekas, Boglárka Mária Shilling-Tóth, Péter Ecsédi, Pál Stráner, László Nyitray, András Perczel:
Evaluation of an Affinity-Enhanced Anti-SARS-CoV2 Nanobody Design Workflow Using Machine Learning and Molecular Dynamics. 7626-7638 - Zhengdong Xu, Jiaxing Tang, Yehong Gong, Jianxin Zhang, Yu Zou:
Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP. 7639-7649 - Olivier Beyens, Sam Corthaut, Sarah Peeters, Pieter Van Der Veken, Ingrid De Meester, Hans De Winter:
Cosolvent Molecular Dynamics Applied to DPP4, DPP8 and DPP9: Reproduction of Important Binding Features and Use in Inhibitor Design. 7650-7665 - Kexin Xu, Zhe Wang, Sutong Xiang, Rongfan Tang, Qirui Deng, Jingxuan Ge, Zhiliang Jiang, Kaimo Yang, Tingjun Hou, Huiyong Sun:
Characterizing the Cooperative Effect of PROTAC Systems with End-Point Binding Free Energy Calculation. 7666-7678 - Tomasz M. Wróbel, Damian Bartuzi, Agnieszka A. Kaczor:
Secondary Binding Site of CYP17A1 in Enhanced Sampling Simulations. 7679-7686 - Shayantan Chaudhuri, David M. Rogers, Christopher J. Hayes, Katherine Inzani, Jonathan D. Hirst:
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors. 7687-7697 - Yun-Peng Wang, Leif A. Eriksson, Ru-Bo Zhang:
Mechanism of Dual-Site Recognition in a Classic DNA Aptamer. 7698-7708 - Liang Xu, Hyunbum Jang, Ruth Nussinov:
Capturing Autoinhibited PDK1 Reveals the Linker's Regulatory Role, Informing Innovative Inhibitor Design. 7709-7724 - Bo Feng, Hui Yu, Xu Dong, Alejandro Díaz-Holguín, Albert A. Antolin, Huabin Hu:
Combining Data-Driven and Structure-Based Approaches in Designing Dual PARP1-BRD4 Inhibitors for Breast Cancer Treatment. 7725-7742 - Erik B. Nordquist, Mingtian Zhao, Anmol Kumar, Alexander D. MacKerell Jr.:
Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots. 7743-7757 - Zhao Dai, Xiaocong Pang, Nan Chen, Xiude Fan, Wei Liu, Jinman Liu, Zhuang Chen, Shuhuan Fang, Chuipu Cai, Jiansong Fang:
Network Medicine Approach Unravels Endophenotype Signature in Alzheimer's Disease through Large-Scale Comparative Proteomics Analysis: Vascular Dysfunction as a Prime Example. 7758-7771 - Wanling Gao, Jun Zhao, Jianfeng Gui, Zehan Wang, Jie Chen, Zhenyu Yue:
Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial Peptides. 7772-7785 - Fubin Chang, Lamei Liu, Fangrui Hu, Xiaohan Sun, Yingchun Zhao, Na Zhang, Chunhua Li:
RNAfcg: RNA Flexibility Prediction Based on Topological Centrality and Global Features. 7786-7792 - Jie Pan, Guangming Zhang, Yong Yang, Wenli Yang, Ning Mao, Zhuhong You, Jie Feng, Shiwei Wang, Yanmei Sun:
MHIPM: Accurate Prediction of Microbe-Host Interactions Using Multiview Features from a Heterogeneous Microbial Network. 7793-7805 - Ping Xuan, Chunhong Guan, Sentao Chen, Jing Gu, Xiuju Wang, Toshiya Nakaguchi, Tiangang Zhang:
Gating-Enhanced Hierarchical Structure Learning in Hyperbolic Space and Multi-scale Neighbor Topology Learning in Euclidean Space for Prediction of Microbe-Drug Associations. 7806-7815 - Anna Ranaudo, Marco Giulini, Angela Pelissou Ayuso, Alexandre M. J. J. Bonvin:
Modeling Protein-Glycan Interactions with HADDOCK. 7816-7825 - Yunjiang Zhang, Shuyuan Li, Kong Meng, Shaorui Sun:
Correction to "Machine Learning for Sequence and Structure-Based Protein-Ligand Interaction Prediction". 7826
Volume 64, Number 20, 2024
- Yulei Wang, Kaiqiang He, Dehua Dong, Jinxing Gu, Jefferson Zhe Liu, Yuxiang Wang:
HexagonRingCalculator: A Handy Code for Hexagonal Ring Characterization in Atomistic Simulations. 7827-7832 - Waqar Ahmad, Kil To Chong, Hilal Tayara:
GGAS2SN: Gated Graph and SmilesToSeq Network for Solubility Prediction. 7833-7843 - Huseyin Tunc, Sumeyye Yilmaz, Busra Nur Darendeli Kiraz, Murat Sari, Seyfullah Enes Kotil, Özge Sensoy, Serdar Durdagi:
Improving Predictive Efficacy for Drug Resistance in Novel HIV-1 Protease Inhibitors through Transfer Learning Mechanisms. 7844-7863 - Mithony Keng, Kenneth M. Merz Jr.:
Eliminating the Deadwood: A Machine Learning Model for CCS Knowledge-Based Conformational Focusing for Lipids. 7864-7872 - Shuya Nakata, Yoshiharu Mori, Shigenori Tanaka:
Navigating Ultralarge Virtual Chemical Spaces with Product-of-Experts Chemical Language Models. 7873-7884 - Zhixin Dou, Jiaxin He, Chao Han, Xiuyun Wu, Lin Wan, Jian Yang, Yanwei Zheng, Bin Gong, Lushan Wang:
qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics. 7885-7894 - Xin Wang, Liangliang Huang, Shuozhi Xu, Kun Lu:
How Does a Generative Large Language Model Perform on Domain-Specific Information Extraction?─A Comparison between GPT-4 and a Rule-Based Method on Band Gap Extraction. 7895-7904 - Kamen P. Petrov, Andreas Bender:
An Open-Source Implementation of the Scaffold Identification and Naming System (SCINS) and Example Applications. 7905-7916 - Jessica Braun, Paul Katzberger, Gregory A. Landrum, Sereina Riniker:
Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings. 7917-7924 - Andrzej Eilmes, Miroslaw Jablonski:
Behavior of Trapped Molecules in Lantern-Like Carcerand Superphanes. 7925-7937 - Franz Waibl, Fabio Casagrande, Fabian Dey, Sereina Riniker:
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents. 7938-7948 - Fiona L. Kearns, Mia A. Rosenfeld, Rommie E. Amaro:
Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins. 7949-7965 - Andrew M. Stokely, Lane W. Votapka, Marcus T. Hock, Abigail E. Teitgen, James Andrew McCammon, Andrew D. McCulloch, Rommie E. Amaro:
NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. 7966-7976 - Hugo A. Perez, Zhe Wang, Bernard S. Gerstman, Jin He, Prem Chapagain:
Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation. 7977-7986 - Yinghui Feng, Yalong Cong, Yue Zhao, Chuanxi Zhang, Hucheng Song, Bohuan Fang, Furong Yang, Huitu Zhang, John Z. H. Zhang, Lujia Zhang:
"Blade of Polarized Water Molecule" Is the Key to Hydrolase Catalysis Regulation. 7987-7997 - Jingyi Yang, Beibei Fu, Rongpei Gou, Xiaoyuan Lin, Haibo Wu, Weiwei Xue:
Molecular Mechanism-Driven Discovery of Novel Small Molecule Inhibitors against Drug-Resistant SARS-CoV-2 Mpro Variants. 7998-8009 - Shayon Bhattacharya, Liang Xu, Lily Arrué, Tim Bartels, Damien Thompson:
Conformational Selection of α-Synuclein Tetramers at Biological Interfaces. 8010-8023 - Gangtong Huang, Zhiyuan Song, Yun Xu, Yunxiang Sun, Feng Ding:
Deciphering the Morphological Difference of Amyloid-β Fibrils in Familial and Sporadic Alzheimer's Diseases. 8024-8033 - Antonella Ciancetta, Davide Malfacini, Matteo Gozzi, Erika Marzola, Riccardo Camilotto, Girolamo Calò, Remo Guerrini:
A Multi-Angle Approach to Predict Peptide-GPCR Complexes: The N/OFQ-NOP System as a Successful AlphaFold Application Case Study. 8034-8051 - Adam Bair, Natalie Printy, So Hee Choi, Joshua Wilkinson, Joseph O'brien, Brian Myers, David Roman, Tarek M. Mahfouz:
In Silico Design of Novel RGS2-Galpha-q Interaction Inhibitors with Anticancer Activity. 8052-8062 - Sondos Musleh, Irfan Alibay, Philip C. Biggin, Richard A. Bryce:
Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations. 8063-8073 - Wenying He, Yu Han, Yun Zuo, Yude Bai, Fei Guo:
NBCR-ac4C: A Deep Learning Framework Based on Multivariate BERT for Human mRNA N4-Acetylcytidine Sites Prediction. 8074-8081
Volume 64, Number 21, 2024
- Alexander S. Shved, Blake Ocampo, Elena S. Burlova, Casey L. Olen, N. Ian Rinehart, Scott E. Denmark:
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction. 8083-8090 - João Gabriel Gralha, André Silva Pimentel:
Gotcha GPT: Ensuring the Integrity in Academic Writing. 8091-8097 - Rasha Atwi, Ye Wang, Simone Sciabola, Adam Antoszewski:
ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring. 8098-8104 - Caiqin Yan, Zhihong Liu, Yiming Bai, Zhe Wang, Jiansong Fang, Ailin Liu:
3DSTarPred: A Web Server for Target Prediction of Bioactive Small Molecules Based on 3D Shape Similarity. 8105-8112 - Andrius Bernatavicius, Martin Sícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuss, Gerard J. P. van Westen:
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models. 8113-8122 - Laust Moesgaard, Jacob Kongsted:
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries. 8123-8130 - Yan Liu, Yiming Mo, Youwei Cheng:
Uncertainty Qualification for Deep Learning-Based Elementary Reaction Property Prediction. 8131-8141 - Joshua Hesse, Davide Boldini, Stephan A. Sieber:
Machine Learning-Driven Data Valuation for Optimizing High-Throughput Screening Pipelines. 8142-8152 - Yili Chen, Zheng Wan, Yangyang Li, Xiao He, Xian Wei, Jun Han:
Graph Curvature Flow-Based Masked Attention. 8153-8163 - Shu Liu, Lu Peng, Liuqing Chen, Linjie Que, Wenqingqing Kang, Xiaojun Hu, Jun Ma, Zengru Di, Yu Liu:
Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations. 8164-8175 - Sonja Peter, Lydia Siragusa, Morgan Thomas, Tommaso Palomba, Simon Cross, Noel M. O'boyle, Dávid Bajusz, György G. Ferenczy, György M. Keserü, Giovanni Bottegoni, Brian Joseph Bender, I-Jen Chen, Chris de Graaf:
Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential. 8176-8192 - Charalampos G. Livas, Pantelis N. Trikalitis, George E. Froudakis:
MOFSynth: A Computational Tool toward Synthetic Likelihood Predictions of MOFs. 8193-8200 - Daniel P. Devore, Kevin L. Shuford:
Data and Molecular Fingerprint-Driven Machine Learning Approaches to Halogen Bonding. 8201-8214 - Emile de Bruyn, Anton Emil Dorn, Giulia Rossetti, Claudio Fernandez, Tiago F. Outeiro, Jörg B. Schulz, Paolo Carloni:
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution. 8215-8226 - Niccolò Bruciaferri, Jérôme Eberhardt, Manuel A. Llanos, Johannes R. Loeffler, Matthew Holcomb, Monica L. Fernández-Quintero, Diogo Santos-Martins, Andrew B. Ward, Stefano Forli:
CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis. 8227-8235 - Alessandro Berselli, Maria Cristina Menziani, Francesco Muniz-Miranda:
Structure and Energetics of PET-Hydrolyzing Enzyme Complexes: A Systematic Comparison from Molecular Dynamics Simulations. 8236-8257 - Neha Vithani, She Zhang, Jeffrey P. Thompson, Lara A. Patel, Alex Demidov, Junchao Xia, Alexander Balaeff, Ahmet Mentes, Yelena A. Arnautova, Anna Kohlmann, J. David Lawson, Anthony Nicholls, A. Geoffrey Skillman, David N. LeBard:
Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS G12D. 8258-8273 - Francesca Scantamburlo, Ionica Masgras, Francesco Ciscato, Claudio Laquatra, Francesco Frigerio, Fabrizio Cinquini, Silvia Pavoni, Alice Triveri, Elena Frasnetti, Stefano A. Serapian, Giorgio Colombo, Andrea Rasola, Elisabetta Moroni:
Design and Test of Molecules that Interfere with the Recognition Mechanisms between the SARS-CoV-2 Spike Protein and Its Host Cell Receptors. 8274-8282 - Berna Dogan, Serdar Durdagi:
Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations. 8283-8298 - Michele Roggia, Benito Natale, Giorgio Amendola, Nicola Grasso, Salvatore Di Maro, Sabrina Taliani, Sabrina Castellano, Serena Concetta Rita Reina, Erica Salvati, Jussara Amato, Sandro Cosconati:
Discovering Dually Active Anti-cancer Compounds with a Hybrid AI-structure-based Approach. 8299-8309 - Javad Deylami, Shu Sin Chng, Ee Hou Yong:
Elucidating Antibiotic Permeation through the Escherichia coli Outer Membrane: Insights from Molecular Dynamics. 8310-8321 - Guishen Wang, Hui Feng, Mengyan Du, Yuncong Feng, Chen Cao:
Multimodal Representation Learning via Graph Isomorphism Network for Toxicity Multitask Learning. 8322-8338 - Gabriela da Rosa, Leandro Grille, Pablo D. Dans:
Ramachandran-like Conformational Space for DNA. 8339-8348 - Wenjing Yin, Shudong Wang, Yuanyuan Zhang, Sibo Qiao, Wenhao Wu, Hengxiao Li:
Multirelational Hypergraph Representation Learning for Predicting circRNA-miRNA Associations. 8349-8360 - Yu Li, Zhu-Hong You, Yang Yuan, Cheng-Gang Mi, Yu-An Huang, Hai-Cheng Yi, Lin-Xuan Hou:
Integrated Knowledge Graph and Drug Molecular Graph Fusion via Adversarial Networks for Drug-Drug Interaction Prediction. 8361-8372
Volume 64, Number 22, 2024
- Dmitry S. Boichenko, Nikita I. Kolomoets, Daniil A. Boiko, Alexey S. Galushko, Alexandra V. Posvyatenko, Andrey E. Kolesnikov, Ksenia S. Egorova, Valentine P. Ananikov:
Build-a-Bio-Strip: An Online Platform for Rapid Toxicity Assessment in Chemical Synthesis. 8373-8378 - Jessica Lanini, Minh Tam Davide Huynh, Gaetano Scebba, Nadine Schneider, Raquel Rodríguez-Pérez:
UNIQUE: A Framework for Uncertainty Quantification Benchmarking. 8379-8386 - Bibhu Prasad Behera, Hemangini Naik, V. Badireenath Konkimalla:
Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid. 8387-8395 - Benjamin Ries, Richard J. Gowers, Hannah M. Baumann, David W. H. Swenson, Michael M. Henry, James R. B. Eastwood, Irfan Alibay, David L. Mobley:
Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations. 8396-8403 - Prashant Sinha, Ablokit Joshi, Rik Dey, Shikhar Misra:
Machine-Learning-Assisted Materials Discovery from Electronic Band Structure. 8404-8413 - Jiahao Fan, Ziyao Li, Eric Alcaide, Guolin Ke, Huaqing Huang, Weinan E:
Accurate Conformation Sampling via Protein Structural Diffusion. 8414-8426 - Yujing Zhao, Lei Zhang, Jian Du, Qingwei Meng, Li Zhang, Heshuang Wang, Liang Sun, Qilei Liu:
Mixture-of-Experts Based Dissociation Kinetic Model for De Novo Design of HSP90 Inhibitors with Prolonged Residence Time. 8427-8439 - Yuzhi Xu, Xinxin Liu, Wei Xia, Jiankai Ge, Cheng-Wei Ju, Haiping Zhang, John Z. H. Zhang:
ChemXTree: A Feature-Enhanced Graph Neural Network-Neural Decision Tree Framework for ADMET Prediction. 8440-8452 - Zhan Si, Deguang Liu, Wan Nie, Jingjing Hu, Chen Wang, Tingting Jiang, Haizhu Yu, Yao Fu:
Data-Based Prediction of Redox Potentials via Introducing Chemical Features into the Transformer Architecture. 8453-8463 - Mauricio Cafiero:
Transformer-Decoder GPT Models for Generating Virtual Screening Libraries of HMG-Coenzyme A Reductase Inhibitors: Effects of Temperature, Prompt Length, and Transfer-Learning Strategies. 8464-8480 - Gustav Olanders, Giulia Testa, Alessandro Tibo, Eva Nittinger, Christian Tyrchan:
Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites. 8481-8494 - Alejandro Gómez-García, Daniel A Acuña Jiménez, William J. Zamora, Haruna L. Barazorda-Ccahuana, Miguel Á. Chávez-Fumagalli, Marilia Valli, Adriano D. Andricopulo, Vanderlan da S. Bolzani, Dionisio A Olmedo, Pablo N. Solís, Marvin J. Núñez, Johny R. Rodríguez Pérez, Hoover A. Valencia Sánchez, Héctor F. Cortés Hernández, Oscar M. Mosquera Martinez, José L. Medina-Franco:
Latin American Natural Product Database (LANaPDB): An Update. 8495-8509 - Andrés Halabi Diaz, Mario Duque-Noreña, Elizabeth Rincón, Eduardo Chamorro:
Synergizing Machine Learning, Conceptual Density Functional Theory, and Biochemistry: No-Code Explainable Predictive Models for Mutagenicity in Aromatic Amines. 8510-8520 - Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, Jan Beránek, Francois Berenger, Albina Bolotokova, Guillaume Bret, Marko Breznik, Emanuele Carosati, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira:
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. 8521-8536 - Chengwei Dong, Yupeng Huang, Xiaohan Lin, Hong Zhang, Yi Qin Gao:
DSDPFlex: Flexible-Receptor Docking with GPU Acceleration. 8537-8548 - Gabriel T. Galdino, Olivier Mailhot, Rafael Najmanovich:
Understanding and Predicting Ligand Efficacy in the μ-Opioid Receptor through Quantitative Dynamical Analysis of Complex Structures. 8549-8561 - Ioannis Gkekas, Sotiris Katsamakas, Stelios K. Mylonas, Theano Fotopoulou, George Epsilon. Magoulas, Alia Cristina Tenchiu, Marios Dimitriou, Apostolos Axenopoulos, Nafsika Rossopoulou, Simona Kostova, Erich E. Wanker, Theodora Katsila, Demetris Papahatjis, Vassilis G. Gorgoulis, Maria Koufaki, Ioannis Karakasiliotis, Theodora Calogeropoulou, Petros Daras, Spyros Petrakis:
AI Promoted Virtual Screening, Structure-Based Hit Optimization, and Synthesis of Novel COVID-19 S-RBD Domain Inhibitors. 8562-8585 - Alec H. Follmer, Thomas L. Poulos:
Application of the Linear Interaction Energy Method to Nitric Oxide Synthase Structure-Based Inhibitor Design. 8586-8594 - Simone Aureli, Francesco Bellina, Valerio Rizzi, Francesco Luigi Gervasio:
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study. 8595-8603 - Yuanming Cao, Pengxuan Xia, Yanyan Zhu, Qingjie Zhao, Huiyu Li:
The Physical Driving Forces of Conformational Transition for TTR91-96 with Proline Mutations. 8604-8615 - Fengjuan Huang, Jiajia Yan, Huan Xu, Ying Wang, Xiaohan Zhang, Yu Zou, Jiangfang Lian, Feng Ding, Yunxiang Sun:
Exploring the Impact of Physiological C-Terminal Truncation on α-Synuclein Conformations to Unveil Mechanisms Regulating Pathological Aggregation. 8616-8627 - Máté Sulyok-Eiler, Veronika Harmat, András Perczel:
Unravelling the Complexity of Amyloid Peptide Core Interfaces. 8628-8640 - Tiyao Liu, Shudong Wang, Yuanyuan Zhang, Yunyin Li, Yingye Liu, Shiyuan Huang:
TIWMFLP: Two-Tier Interactive Weighted Matrix Factorization and Label Propagation Based on Similarity Matrix Fusion for Drug-Disease Association Prediction. 8641-8654 - Sumit Tarafder, Debswapna Bhattacharya:
lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures. 8655-8664
Volume 64, Number 23, 2024
- Ernesto Contreras-Torres, Yovani Marrero-Ponce:
MD-LAIs Software: Computing Whole-Sequence and Amino Acid-Level "Embeddings" for Peptides and Proteins. 8665-8672 - Qingqing Yang, Wennuo Xu, Xiaodong Sun, Qin Chen, Bing Niu:
The Application of Machine Learning in Doping Detection. 8673-8683 - Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein:
Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling. 8684-8704 - Peiyao Li, Lan Hua, Zhechao Ma, Wenbo Hu, Ye Liu, Jun Zhu:
Conformalized Graph Learning for Molecular ADMET Property Prediction and Reliable Uncertainty Quantification. 8705-8717 - Hengjian Jia, Gabriele C. Sosso:
Transparent Machine Learning Model to Understand Drug Permeability through the Blood-Brain Barrier. 8718-8728 - Romanos Fasoulis, Georgios Paliouras, Lydia E. Kavraki:
RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models. 8729-8742 - Nicholas B. Smith, Anna L. Garden:
A Divide-and-Conquer Approach to Nanoparticle Global Optimisation Using Machine Learning. 8743-8755 - Lucía Morán-González, Jørn Eirik Betten, Hannes Kneiding, David Balcells:
AABBA Graph Kernel: Atom-Atom, Bond-Bond, and Bond-Atom Autocorrelations for Machine Learning. 8756-8769 - Myeonghun Lee, Taehyun Park, Kyoungmin Min:
Matini-Net: Versatile Material Informatics Research Framework for Feature Engineering and Deep Neural Network Design. 8770-8783 - Hengwei Chen, Jürgen Bajorath:
Combining a Chemical Language Model and the Structure-Activity Relationship Matrix Formalism for Generative Design of Potent Compounds with Core Structure and Substituent Modifications. 8784-8795 - Zhiyuan Zhou, Yueming Yin, Hao Han, Yiping Jia, Jun Hong Koh, Adams Wai-Kin Kong, Yuguang Mu:
ProAffinity-GNN: A Novel Approach to Structure-Based Protein-Protein Binding Affinity Prediction via a Curated Data Set and Graph Neural Networks. 8796-8808 - Li Liang, Yunxin Duan, Chen Zeng, Boheng Wan, Huifeng Yao, Haichun Liu, Tao Lu, Yanmin Zhang, Yadong Chen, Jun Shen:
CPIScore: A Deep Learning Approach for Rapid Scoring and Interpretation of Protein-Ligand Binding Interactions. 8809-8823 - Fatemeh Etezadi, Shunichi Ito, Kosuke Yasui, Rodi Kado Abdalkader, Itsunari Minami, Motonari Uesugi, Ganesh Namasivayam Pandian, Haruko Nakano, Atsushi Nakano, Daniel M. Packwood:
Molecular Design for Cardiac Cell Differentiation Using a Small Data Set and Decorated Shape Features. 8824-8837 - Jonathan W. Zheng, Ivo Leito, William H. Green Jr.:
Widespread Misinterpretation of pKa Terminology for Zwitterionic Compounds and Its Consequences. 8838-8847 - David Schaller, Clara D. Christ, John D. Chodera, Andrea Volkamer:
Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. 8848-8858 - Donya Ohadi, Kiran Kumar, Suchitra Ravula, Renee L. DesJarlais, Mark Seierstad, Amy Y. Shih, Michael D. Hack, Jamie M. Schiffer:
Input Pose is Key to Performance of Free Energy Perturbation: Benchmarking with Monoacylglycerol Lipase. 8859-8869 - Chris Zhang, Meghan Osato, David L. Mobley:
Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling. 8870-8879 - Xibing He, Viet Hoang Man, Jie Gao, Junmei Wang:
Effects of All-Atom and Coarse-Grained Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of a Tau K18 Monomer. 8880-8891 - Abhishek Bera, Pritish Joshi, Niladri Patra:
Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism. 8892-8908 - Christian Hölzer, Rick Oerder, Stefan Grimme, Jan Hamaekers:
ConfRank: Improving GFN-FF Conformer Ranking with Pairwise Training. 8909-8925 - Thomas J. Summers, Difan Zhang, Josiane A. Sobrinho, Ana de Bettencourt-Dias, Roger Rousseau, Vassiliki-Alexandra Glezakou, David C. Cantu:
Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution. 8926-8936 - Ammaar A. Saeed, Margaret A. Klureza, Doeke Hekstra:
Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens. 8937-8951 - Mingqing Liu, Xuechun Meng, Yiyang Mao, Hongqi Li, Ji Liu:
ReduMixDTI: Prediction of Drug-Target Interaction with Feature Redundancy Reduction and Interpretable Attention Mechanism. 8952-8962 - Levente M. Mihalovits, Tibor V. Szalai, Dávid Bajusz, György M. Keserü:
Exploring Chemical Spaces in the Billion Range: Is Docking a Computational Alternative to DNA-Encoded Libraries? 8963-8979 - Tibor Viktor Szalai, Dávid Bajusz, Rita Börzsei, Balázs Zoltán Zsidó, Janez Ilas, György G. Ferenczy, Csaba Hetényi, György M. Keserü:
Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments. 8980-8998 - Wagner Rocha, Leo Liberti, Antonio Mucherino, Thérèse E. Malliavin:
Influence of Stereochemistry in a Local Approach for Calculating Protein Conformations. 8999-9008 - Jingzhi Wang, Sida Qin, Xiaohui Zhang, Jixin Zhi:
Identification of Macrophage-Associated Novel Drug Targets in Atherosclerosis Based on Integrated Transcriptome Features. 9009-9020
Volume 64, Number 24, 2024
- Gergely Zahoránszky-Köhalmi, Brandon Walker, Nathan Miller, Brett Yang, Dhatri V. L. Penna, Jessica Maine, Timothy Sheils, Ke Wang, Jennifer King, Hythem Sidky, Sridhar Vuyyuru, Jeyaraman Soundarajan, Samuel G. Michael, Alexander G. Godfrey, Tudor I. Oprea:
SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting. 9021-9026 - Jochen Sieg, Christian Feldmann, Jennifer Hemmerich, Conrad Stork, Frederik Sandfort, Philipp Eiden, Miriam Mathea:
MolPipeline: A Python Package for Processing Molecules with RDKit in Scikit-learn. 9027-9033 - Alexander Kravberg, Didier Devaurs, Anastasiia Varava, Lydia E. Kavraki, Danica Kragic:
MoleQCage: Geometric High-Throughput Screening for Molecular Caging Prediction. 9034-9039 - Jessica Valero-Rojas, Camilo Ramírez-Sánchez, Laura Pacheco-Paternina, Paulina Valenzuela-Hormazabal, Fernanda I. Saldivar-González, Paula Santana, Janneth González, Tatiana Gutiérrez-Bunster, Alejandro Valdés-Jiménez, David Ramírez:
AlzyFinder: A Machine-Learning-Driven Platform for Ligand-Based Virtual Screening and Network Pharmacology. 9040-9047 - Zhihan Zhang, Dongliang Ke, Chengshan Jin, Weiyu Zhou, Xiaolin Pan, Yueqing Zhang, Xingyu Wang, Xudong Xiao, Changge Ji:
MacGen: A Web Server for Structure-Based Macrocycle Design. 9048-9055 - Francisco Lucas Feitosa, Victoria F. Cabral, Igor Henrique Sanches, Sabrina Silva-Mendonca, Joyce V. V. B. Borba, Rodolpho C. Braga, Carolina Horta Andrade:
Cyto-Safe: A Machine Learning Tool for Early Identification of Cytotoxic Compounds in Drug Discovery. 9056-9062 - Apoorva Mathur, Rikhia Ghosh, Ariane Nunes-Alves:
Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells. 9063-9081 - Jie Li, Oufan Zhang, Kunyang Sun, Yingze Wang, Xingyi Guan, Dorian Bagni, Mojtaba Haghighatlari, Fiona L. Kearns, Conor D. Parks, Rommie E. Amaro, Teresa Head-Gordon:
Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. 9082-9097 - Duancheng Zhao, Yanhong Zhang, Yihao Chen, Biaoshun Li, Wenguang Zhou, Ling Wang:
Highly Accurate and Explainable Predictions of Small-Molecule Antioxidants for Eight In Vitro Assays Simultaneously through an Alternating Multitask Learning Strategy. 9098-9110 - Akash Saraswat, Utsav Sharma, Aryan Gandotra, Lakshit Wasan, Sainithin Artham, Arijit Maitra, Bipin Singh:
Pred-AHCP: Robust Feature Selection-Enabled Sequence-Specific Prediction of Anti-Hepatitis C Peptides via Machine Learning. 9111-9124 - Muhammad-Shahid Malik, Yan-Yun Chang, Yu-Chen Liu, Van-The Le, Yu-Yen Ou:
MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks. 9125-9134 - Fanhao Wang, Yuzhe Wang, Laiyi Feng, Changsheng Zhang, Luhua Lai:
Target-Specific De Novo Peptide Binder Design with DiffPepBuilder. 9135-9149 - Lemnaro Jamir, P. Hariprasad:
Employing Machine Learning Models to Predict Potential α-Glucosidase Inhibitory Plant Secondary Metabolites Targeting Type-2 Diabetes and Their In Vitro Validation. 9150-9162 - Frank Filip Steinbauer, Thorsten Lehr, Andreas Reichel:
Exploring the Potential of Adaptive, Local Machine Learning in Comparison to the Prediction Performance of Global Models: A Case Study from Bayer's Caco-2 Permeability Database. 9163-9172 - Long D. Nguyen, Quang H. Nguyen, Quang H. Trinh, Binh P. Nguyen:
From SMILES to Enhanced Molecular Property Prediction: A Unified Multimodal Framework with Predicted 3D Conformers and Contrastive Learning Techniques. 9173-9195 - Jordy Schifferstein, Andrius Bernatavicius, Antonius P. A. Janssen:
Docking-Informed Machine Learning for Kinome-wide Affinity Prediction. 9196-9204 - Zixin Zhuang, Amanda S. Barnard:
Property Prediction for Complex Compounds Using Structure-Free Mendeleev Encoding and Machine Learning. 9205-9214 - Jonghyun Lee, Dokyoon Kim, Dae Won Jun, Yun Kim:
Multimodal Fusion-Based Lightweight Model for Enhanced Generalization in Drug-Target Interaction Prediction. 9215-9226 - Jingtian Xu, Yong Wang:
Generating Multistate Conformations of P-type ATPases with a Conditional Diffusion Model. 9227-9239 - Hongxiang Li, Xuan Liu, Guangde Jiang, Huimin Zhao:
Chemoenzymatic Synthesis Planning Guided by Reaction Type Score. 9240-9248 - Chureh Atasi, Joseph Kern, Rampi Ramprasad:
Design of Recyclable Plastics with Machine Learning and Genetic Algorithm. 9249-9259 - Haoyang Liu, Yifei Qin, Zhangming Niu, Mingyuan Xu, Jiaqiang Wu, Xianglu Xiao, Jinping Lei, Ting Ran, Hongming Chen:
How Good are Current Pocket-Based 3D Generative Models?: The Benchmark Set and Evaluation of Protein Pocket-Based 3D Molecular Generative Models. 9260-9275 - Ruihong Wang, Xiao Liang, Yi Zhao, Wenjun Xue, Guizhao Liang:
UniBioPAN: A Novel Universal Classification Architecture for Bioactive Peptides Inspired by Video Action Recognition. 9276-9285 - Jinfu Peng, Li Fu, Guoping Yang, Dongsheng Cao:
Advanced AI-Driven Prediction of Pregnancy-Related Adverse Drug Reactions. 9286-9298 - Steven Kearnes, Patrick Riley:
Ordinal Confidence Level Assignments for Regression Model Predictions. 9299-9305 - Qing Liu, Dakuo He, Mengmeng Fan, Jinpeng Wang, Zeyu Cui, Hao Wang, Yan Mi, Ning Li, Qingqi Meng, Yue Hou:
Prediction and Interpretation Microglia Cytotoxicity by Machine Learning. 9306-9326 - Muhammad Irfan Khawar, Muhammad Arshad, Eric P. Achterberg, Deedar Nabi:
Streamlining Linear Free Energy Relationships of Proteins through Dimensionality Analysis and Linear Modeling. 9327-9340 - Elena Xerxa, Martin Vogt, Jürgen Bajorath:
Influence of Data Curation and Confidence Levels on Compound Predictions Using Machine Learning Models. 9341-9349 - Takato Ue, Akinori Sato, Tomoyuki Miyao:
Analog Accessibility Score (AAscore) for Rational Compound Selection. 9350-9360 - Zhe Wang, Jianping Wu, Mengjun Zheng, Chenchen Geng, Borui Zhen, Wei Zhang, Hui Wu, Zhengyang Xu, Gang Xu, Si Chen, Xiang Li:
StaPep: An Open-Source Toolkit for Structure Prediction, Feature Extraction, and Rational Design of Hydrocarbon-Stapled Peptides. 9361-9373 - Martin Ljubic, Andrej Perdih, Jure Borisek:
All-Atom Simulations Reveal the Effect of Membrane Composition on the Signaling of the NKG2A/CD94/HLA-E Immune Receptor Complex. 9374-9387 - Ian Dunn, Somayeh Pirhadi, Yao Wang, Smmrithi Ravindran, Carter Concepcion, David Ryan Koes:
CACHE Challenge #1: Docking with GNINA Is All You Need. 9388-9396 - Daniel B. K. Chu, David A. González-Narváez, Ralf Meyer, Aditya Nandy, Heather J. Kulik:
Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery. 9397-9412 - Tristan Bereau, Luis J. Walter, Joseph F. Rudzinski:
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations. 9413-9423 - Richard Overstreet, Dennis G. Thomas, John R. Cort:
NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials. 9424-9432 - Negin Forouzesh, Fatemeh Ghafouri, Igor S. Tolokh, Alexey V. Onufriev:
Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent. 9433-9448 - Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama, Akifumi Kato, Yuji Mochizuki, Tatsuya Nakano, Teruki Honma, Kaori Fukuzawa:
Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites. 9449-9458 - Deng Li, Mona S. Minkara:
Comparative Assessment of Water Models in Protein-Glycan Interaction: Insights from Alchemical Free Energy Calculations and Molecular Dynamics Simulations. 9459-9473 - Sofia Cresca, Angela Parise, Alessandra Magistrato:
Assessing the Mechanism of Rac1b: An All-Atom Simulation Study of the Alternative Spliced Variant of Rac1 Small Rho GTPase. 9474-9486 - Yi Li, Qin-Wei Xu, Guo-Lei Jian, Xiao-Ling Zhang, Hua Wang:
Improved and Interpretable Prediction of Cytochrome P450-Mediated Metabolism by Molecule-Level Graph Modeling and Subgraph Information Bottlenecks. 9487-9500 - Muya Xiong, Tianqing Nie, Zhewen Li, Meiyi Hu, Haixia Su, Hangchen Hu, Yechun Xu, Qiang Shao:
Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations. 9501-9516 - Zheng Zhao, Philip E. Bourne:
Exploring Extended Warheads toward Developing Cysteine-Targeted Covalent Kinase Inhibitors. 9517-9527 - Tian-Hua Wei, Shuang-Shuang Zhou, Xiao-Long Jing, Jia-Chuan Liu, Meng Sun, Zong-Hao Zhao, Qing-Qing Li, Zi-Xuan Wang, Jin Yang, Yun Zhou, Xue Wang, Cheng-Xiao Ling, Ning Ding, Xin Xue, Yan-Cheng Yu, Xiao-Long Wang, Xiao-Ying Yin, Shan-Liang Sun, Peng Cao, Nian-Guang Li, Zhi-Hao Shi:
Kinase-Bench: Comprehensive Benchmarking Tools and Guidance for Achieving Selectivity in Kinase Drug Discovery. 9528-9550 - Yunjiong Liu, Peiliang Zhang, Chao Che, Ziqi Wei:
SDDSynergy: Learning Important Molecular Substructures for Explainable Anticancer Drug Synergy Prediction. 9551-9562 - Qilong Wu, Sheng-You Huang:
XDock: A General Docking Method for Modeling Protein-Ligand and Nucleic Acid-Ligand Interactions. 9563-9575 - Renato Soares, Luísa Azevedo, Vitor Vasconcelos, Diogo Pratas, Sergio F. Sousa, João Carneiro:
Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation. 9576-9593 - Guobo Xie, Dayin Li, Zhiyi Lin, Guosheng Gu, Weijun Li, Ruibin Chen, Zhenguo Liu:
HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization. 9594-9608 - Shahid Akbar, Matee Ullah, Ali Raza, Quan Zou, Wajdi Alghamdi:
DeepAIPs-Pred: Predicting Anti-Inflammatory Peptides Using Local Evolutionary Transformation Images and Structural Embedding-Based Optimal Descriptors with Self-Normalized BiTCNs. 9609-9625 - Xiaohua Wang, Ming Zhang, Xibei Yang, Dong-Jun Yu, Fang Ge:
GPTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in G Protein-Coupled Receptors. 9626-9642 - Derek van Tilborg, Alisa Alenicheva, Francesca Grisoni:
Correction to "Exposing the Limitations of Molecular Machine Learning with Activity Cliffs". 9643-9648 - Issar Arab, Kris Laukens, Wout Bittremieux:
Correction to "Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set". 9649-9650 - Martina Piga, Zoltán Varga, Adam Feher, Ferenc Papp, Eva Korpos, Kavya C. Bangera, Rok Frlan, Janez Ilas, Jaka Dernovsek, Tihomir Tomasic, Nace Zidar:
Correction to "Identification of a Novel Structural Class of HV1 Inhibitors by Structure-Based Virtual Screening". 9651
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