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ORCIDJournal of Chemical Information and Modeling, Volume 62
Volume 62, Number 1, January 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Haochuan Chen
, Han Liu, Heying Feng, Haohao Fu, Wensheng Cai, Xueguang Shao, Christophe Chipot:
MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation. 1-8 - Sakari Lätti, Sanna P. Niinivehmas, Olli T. Pentikäinen:
Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. 9-15 - Esther Heid, Jiannan Liu, Andrea Aude, William H. Green Jr.:
Influence of Template Size, Canonicalization, and Exclusivity for Retrosynthesis and Reaction Prediction Applications. 16-26 - Xianjin Xu, Xiaoqin Zou:
Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment. 27-39 - Felsis Angelene Daison, Nitheeshkumar Kumar, Siranjeevi Balakrishnan, Kavyashree Venugopal, Sangamithra Elango, Pandian Sokkar:
Molecular Dynamics Studies on the Bacterial Membrane Pore Formation by Small Molecule Antimicrobial Agents. 40-48 - Philipp Nicolas Depta, Pavel Gurikov, Baldur Schroeter, Attila Forgács, József Kalmár, Geo Paul, Leonardo Marchese, Stefan Heinrich, Maksym Dosta:
DEM-Based Approach for the Modeling of Gelation and Its Application to Alginate. 49-70 - Kiyoshiro Okada, Paul E. Brumby, Kenji Yasuoka:
An Efficient Random Number Generation Method for Molecular Simulation. 71-78 - Jacob M. Litman, Chengwen Liu, Pengyu Y. Ren:
Atomic Polarizabilities for Interactive Dipole Induction Models. 79-87 - Hadrián Montes-Campos, Jesús Carrete, Sebastian Bichelmaier, Luis M. Varela, Georg K. H. Madsen:
A Differentiable Neural-Network Force Field for Ionic Liquids. 88-101 - Gamze Tanriver, Gerald Monard, Saron Catak:
Impact of Deamidation on the Structure and Function of Antiapoptotic Bcl-xL. 102-115 - Austin Clyde, Stephanie Galanie, Daniel W. Kneller, Heng Ma, Yadu N. Babuji, Ben Blaiszik, Alexander Brace, Thomas S. Brettin, Kyle Chard, Ryan Chard, Leighton Coates, Ian T. Foster, Darin Hauner, Vilmos Kertesz, Neeraj Kumar, Hyungro Lee, Zhuozhao Li, André Merzky, Jurgen G. Schmidt, Li Tan, Mikhail Titov, Anda Trifan, Matteo Turilli, Hubertus Van Dam, Srinivas C. Chennubhotla, Shantenu Jha, Andrey Kovalevsky, Arvind Ramanathan, Martha S. Head, Rick Stevens:
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. 116-128 - Maryam Ghasemitarei, Angela Privat-Maldonado, Maksudbek Yusupov, Shadi Rahnama, Annemie Bogaerts, Mohammad Reza Ejtehadi:
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations. 129-141 - Samanta Makurat, Zoe Cournia, Janusz Rak:
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. 142-149 - Jack A. Henderson, Jana Shen:
Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II. 150-158 - Jorge Enrique Hernández González, Lucas N. Alberca, Yordanka Masforrol González, Osvaldo Reyes Acosta, Alan Talevi, Emir Salas-Sarduy:
Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site. 159-175 - Beibei Wang, Changqing Zhong, D. Peter Tieleman:
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes. 176-186 - Juan Xie, Shiwei Wang, Youjun Xu, Minghua Deng, Luhua Lai:
Uncovering the Dominant Motion Modes of Allosteric Regulation Improves Allosteric Site Prediction. 187-195 - Bianca Fiorillo, Silvia Marchianò, Federica Moraca, Valentina Sepe, Adriana Carino, Pasquale Rapacciuolo, Michele Biagioli, Vittorio Limongelli, Angela Zampella, Bruno Catalanotti, Stefano Fiorucci:
Discovery of Bile Acid Derivatives as Potent ACE2 Activators by Virtual Screening and Essential Dynamics. 196-209 - Gian Marco Elisi, Laura Scalvini, Alessio Lodola, Marco Mor, Silvia Rivara:
Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. 210-222 - Zheng Zhao, Lei Xie, Philip E. Bourne:
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants". 223-224
Volume 62, Number 2, January 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Alejandro Varela-Rial, Iain Maryanow, Maciej Majewski, Stefan Doerr, Nikolai Schapin, José Jiménez-Luna, Gianni De Fabritiis:
PlayMolecule Glimpse: Understanding Protein-Ligand Property Predictions with Interpretable Neural Networks. 225-231 - Sorin Muraru, Sebastian Muraru, Florentin Romeo Nitu, Mariana Ionita:
Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods. 232-239 - Jannis Born, Tien Huynh, Astrid Stroobants, Wendy D. Cornell, Matteo Manica:
Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model. 240-257 - Fei Zhu, Feifei Li, Lei Deng, Fanwang Meng, Zhongjie Liang:
Protein Interaction Network Reconstruction with a Structural Gated Attention Deep Model by Incorporating Network Structure Information. 258-273 - José Jiménez-Luna, Miha Skalic, Nils Weskamp:
Benchmarking Molecular Feature Attribution Methods with Activity Cliffs. 274-283 - Mihaela D. Smilova, Peter R. Curran, Chris J. Radoux, Frank von Delft, Jason C. Cole, Anthony R. Bradley, Brian D. Marsden:
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins. 284-294 - Christopher L. Hanselman, Xiangyu Yin, David C. Miller, Chrysanthos E. Gounaris:
MatOpt: A Python Package for Nanomaterials Design Using Discrete Optimization. 295-308 - Solmaz Azimi, Sheenam Khuttan, Joe Z. Wu, Rajat Kumar Pal, Emilio Gallicchio:
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method. 309-323 - Bakar A. Hassan, Jozafina Milicaj, Carlos Andres Ramirez-Mondragon, Yuk Yin Sham, Erika A. Taylor:
Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes. 324-339 - Dhanushka Weerakoon, Rodrigo J. Carbajo, Leonardo De Maria, Christian Tyrchan, Hongtao Zhao:
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex. 340-349 - Kazuki Z. Yamamoto, Nobuaki Yasuo, Masakazu Sekijima:
Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides. 350-358 - Didac Martí, Carlos Alemán, Jon Ainsley, Oscar Ahumada, Juan Torras:
IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study. 359-371 - Jun Chen, Hao Liu, Xiaochen Cui, Zhengxin Li, Hai-Feng Chen:
RNA-Specific Force Field Optimization with CMAP and Reweighting. 372-385 - Shu dong Wang, Leif A. Eriksson, Ru bo Zhang:
Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. 386-398 - Narin Lawan, Ruchanok Tinikul, Panida Surawatanawong, Adrian J. Mulholland, Pimchai Chaiyen:
QM/MM Molecular Modeling Reveals Mechanism Insights into Flavin Peroxide Formation in Bacterial Luciferase. 399-411 - Jiahui Chen, Rui Wang, Nancy Benovich Gilby, Guo-Wei Wei:
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance. 412-422
Volume 62, Number 3, February 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- E. Adrian Henle, Nickolas Gantzler, Praveen K. Thallapally, Xiaoli Z. Fern, Cory M. Simon:
PoreMatMod.jl: Julia Package for in Silico Postsynthetic Modification of Crystal Structure Models. 423-432 - Yunsie Chung, Florence H. Vermeire, Haoyang Wu, Pierre J. Walker, Michael H. Abraham, William H. Green Jr.:
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy. 433-446 - Tobias Harren, Hans Matter, Gerhard Hessler, Matthias Rarey, Christoph Grebner:
Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. 447-462 - Jian Wang, Nikolay V. Dokholyan:
Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. 463-471 - Shuzhe Wang, Kajo Krummenacher, Gregory A. Landrum, Benjamin D. Sellers, Paola Di Lello, Sarah J. Robinson, Bryan Martin, Jeffrey K. Holden, Jeffrey Y. K. Tom, Anastasia C. Murthy, Nataliya Popovych, Sereina Riniker:
Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. 472-485 - Dongping Li, Kexin Jiang, Dan Teng, Zengrui Wu, Weihua Li, Yun Tang, Rui Wang, Guixia Liu:
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking. 486-497 - Wenyi Zhang, Jing Huang:
EViS: An Enhanced Virtual Screening Approach Based on Pocket-Ligand Similarity. 498-510 - Alessandro Nicoli, Andreas Dunkel, Toni Giorgino, Chris de Graaf, Antonella Di Pizio:
Classification Model for the Second Extracellular Loop of Class A GPCRs. 511-522 - Wenqing Li, Jiabin Zhang, Li Guo, Qiantao Wang:
Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations. 523-532 - Francesc Sabanés Zariquiey, Edgar Jacoby, Ann Vos, Herman W. T. van Vlijmen, Gary Tresadern, Jeremy N. Harvey:
Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery. 533-543 - Montserrat Penaloza-Amion, Celso R. C. Rêgo, Wolfgang Wenzel:
Local Electronic Charge Transfer in the Helical Induction of Cis-Transoid Poly(4-carboxyphenyl)acetylene by Chiral Amines. 544-552 - Louis Bellmann, Patrick Penner, Marcus Gastreich, Matthias Rarey:
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. 553-566 - Dalibor Trapl, Martin Krupicka, Vladimír Visnovský, Jana Hozzová, Jaroslav Olha, Ales Krenek, Vojtech Spiwok:
Property Map Collective Variable as a Useful Tool for a Force Field Correction. 567-576 - Rory M. Crean, Christopher R. Pudney, David K. Cole, Marc van der Kamp:
Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA. 577-590 - Samuel J. H. Gaughan, Jonathan D. Hirst, Anna K. Croft, Christof M. Jäger:
Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. 591-601 - Josh Vincent Vermaas, Christopher G. Mayne, Eric Shinn, Emad Tajkhorshid:
Assembly and Analysis of Cell-Scale Membrane Envelopes. 602-617 - Debarati DasGupta, Wallace K. B. Chan, Heather A. Carlson:
Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease. 618-626 - Filip Fratev:
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. 627-631 - Yijing Wang, Xinyi Li, Jingjing Wei, Xue Zhang, Yongjun Liu:
Mechanism of Sugar Ring Contraction and Closure Catalyzed by UDP-d-apiose/UDP-d-xylose Synthase (UAXS). 632-646 - Qianzhen Shao, Yaoyukun Jiang, Zhongyue J. Yang:
EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling. 647-655 - Xiaocong Wang, Lihua Bie, Jun Gao:
Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II. 656-667 - Cecilia Chávez-García, Mikko Karttunen:
Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases. 668-677 - Damien Geslin, Alban Lepailleur, Jean-Luc Manguin, Nhat-Vinh Vo, Jean Luc Lamotte, Bertrand Cuissart, Ronan Bureau:
Deciphering a Pharmacophore Network: A Case Study Using BCR-ABL Data. 678-691 - Xiao Li, Lun Zhang, Jing Xu, Chenyu Liu, Xiaojian Zhang, Amr Abbas Abdelmoneim, Qian Zhang, Jiaqi Ke, Yingnan Zhang, Lei Wang, Fan Yang, Cheng Luo, Jia Jin, Fei Ye:
Identification, Synthesis, and Biological Evaluations of Potent Inhibitors Targeting Type I Protein Arginine Methyltransferases. 692-702 - Gary Tresadern, Kanaka Tatikola, Javier Cabrera, Lingle Wang, Robert Abel, Herman van Vlijmen, Helena Geys:
The Impact of Experimental and Calculated Error on the Performance of Affinity Predictions. 703-717 - Gergely Zahoránszky-Köhalmi, Vishal B. Siramshetty, Praveen Kumar, Manideep Gurumurthy, Busola Grillo, Biju Mathew, Dimitrios Metaxatos, Mark Backus, Tim Mierzwa, Reid Simon, Ivan Grishagin, Laura Brovold, Ewy A. Mathé, Matthew D. Hall, Samuel G. Michael, Alexander G. Godfrey, Jordi Mestres, Lars Juhl Jensen, Tudor I. Oprea:
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. 718-729 - Gen Li, Qing-Qing Dai, Guo-Bo Li:
MeCOM: A Method for Comparing Three-Dimensional Metalloenzyme Active Sites. 730-739 - Hao Li, Yumeng Yan, Xuejun Zhao, Sheng-You Huang:
Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials. 740-750 - (Withdrawn) Retraction of "Challenges in Predicting Aqueous Solubility of Organic Molecules Using the COSMO-RS Model". 751
Volume 62, Number 4, February 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Jade Young, Neerja Garikipati, Jacob D. Durrant:
BINANA 2: Characterizing Receptor/Ligand Interactions in Python and JavaScript. 753-760 - Eugene Lin, Chieh-Hsin Lin, Hsien Yuan Lane:
De Novo Peptide and Protein Design Using Generative Adversarial Networks: An Update. 761-774 - Hiroko X. Kondo, Masanori Fujii, Takuma Tanioka, Yusuke Kanematsu, Takashi Yoshida, Yu Takano:
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. 775-784 - Brajesh K. Rai, Vishnu Sresht, Qingyi Yang, Ray Unwalla, Meihua Tu, Alan M. Mathiowetz, Gregory A. Bakken:
TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics. 785-800 - Seung-gu Kang, Joseph A. Morrone, Jeffrey K. Weber, Wendy D. Cornell:
Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule Generation. 801-816 - André F. Oliveira, Juarez L. F. Da Silva, Marcos G. Quiles:
Molecular Property Prediction and Molecular Design Using a Supervised Grammar Variational Autoencoder. 817-828 - Devon P. Holst, Pascal Friederich, Alán Aspuru-Guzik, Timothy P. Bender:
Updated Calibrated Model for the Prediction of Molecular Frontier Orbital Energies and Its Application to Boron Subphthalocyanines. 829-840 - Jorge L. Castro Angamarca, Raúl Manzanilla Morillo, Thibault Terencio:
Delta Chem: A New Geometric Approach of Porosity for Symmetric Porous Materials. 841-853 - Umesh B. Gadgoli, Sunil Kumar Y. C., Deepak Kumar, Maya Pai, Sravani Pulya, Balaram Ghosh, Onkar Prakash Kulkarni:
Estrogenic Activity of Tetrazole Derivatives Bearing Bisphenol Structures: Computational Studies, Synthesis, and In Vitro Assessment. 854-873 - Owen Madin, Simon Boothroyd, Richard A. Messerly, Josh Fass, John D. Chodera, Michael R. Shirts:
Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. 874-889 - Lukas Krep, Indu Sekhar Roy, Wassja A. Kopp, Felix Schmalz, Can Huang, Kai Leonhard:
Efficient Reaction Space Exploration with ChemTraYzer-TAD. 890-902 - Ana Dreab, Craig A. Bayse:
Molecular Dynamics Simulations of Reduced and Oxidized TFIIIA Zinc Fingers Free and Interacting with 5S RNA. 903-913 - Soumendranath Bhakat, Pär Söderhjelm:
Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. 914-926 - Bianca Villavicencio, Rodrigo Ligabue-Braun, Hugo Verli:
Structural Characteristics of Glycocins: Unraveling the Role of S-Linked Carbohydrates and Other Structural Elements. 927-935 - Baocai Ma, Zuoheng Zhang, Yan Li, Xubo Lin, Ning Gu:
Evaluation of Interactions between SARS-CoV-2 RBD and Full-Length ACE2 with Coarse-Grained Molecular Dynamics Simulations. 936-944 - Naiá Porã Santos, Lucianna Helene Santos, Mariana Torquato Quezado de Magalhães, Jian Lei, Rolf Hilgenfeld, Rafaela Salgado Ferreira, Lucas Bleicher:
Characterization of an Allosteric Pocket in Zika Virus NS2B-NS3 Protease. 945-957 - Cecilia Chávez-García, Jérôme Hénin, Mikko Karttunen:
Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. 958-970 - Yaoxi Chen, Quan Chen, Haiyan Liu:
DEPACT and PACMatch: A Workflow of Designing De Novo Protein Pockets to Bind Small Molecules. 971-985 - Giuseppe Licari, Sepehr Dehghani-Ghahnaviyeh, Emad Tajkhorshid:
Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. 986-996 - Farideh Badichi Akher, Abdolkarim Farrokhzadeh, Neil Ravenscroft, Michelle M. Kuttel:
Deciphering the Mechanism of Binding Selectivity of Chlorofluoroacetamide-Based Covalent Inhibitors toward L858R/T790M Resistance Mutation. 997-1013 - Ilaria Salutari, Amedeo Caflisch:
Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein. 1014-1024 - Shalini Yadav, Sason Shaik, Shakir Ali Siddiqui, Surajit Kalita, Kshatresh Dutta Dubey:
Local Electric Fields Dictate Function: The Different Product Selectivities Observed for Fatty Acid Oxidation by Two Deceptively Very Similar P450-Peroxygenases OleT and BSβ. 1025-1035 - Irina D. Pogozheva, Grant A. Armstrong, Lingyang Kong, Timothy J. Hartnagel, Carly A. Carpino, Stephen E. Gee, Danielle M. Picarello, Amanda S. Rubin, Jumin Lee, Soohyung Park, Andrei L. Lomize, Wonpil Im:
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes. 1036-1051 - Yao Chi Chen, Yu-Hsien Chen, Jon D. Wright, Carmay Lim:
PPI-HotspotDB: Database of Protein-Protein Interaction Hot Spots. 1052-1060 - Anne Labarre, Julia K. Stille, Mihai Burai Patrascu, Andrew Martins, Joshua Pottel, Nicolas Moitessier:
Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds─Challenges and Opportunities. 1061-1077 - Suqing Zheng, Lei Wang, Jun Xiong, Guang Liang, Yong Xu, Fu Lin:
Consensus Prediction of Human Gut Microbiota-Mediated Metabolism Susceptibility for Small Molecules by Machine Learning, Structural Alerts, and Dietary Compounds-Based Average Similarity Methods. 1078-1099 - Sami T. Kurkinen, Jukka V. Lehtonen, Olli T. Pentikäinen, Pekka A. Postila:
Optimization of Cavity-Based Negative Images to Boost Docking Enrichment in Virtual Screening. 1100-1112 - Daniela Trisciuzzi, Lydia Siragusa, Massimo Baroni, Ida Autiero, Orazio Nicolotti, Gabriele Cruciani:
Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions. 1113-1125 - Anu R. Melge, Shraddha Parate, Keechilat Pavithran, Manzoor Koyakutty, C. Gopi Mohan:
Discovery of Anticancer Hybrid Molecules by Supervised Machine Learning Models and in Vitro Validation in Drug Resistant Chronic Myeloid Leukemia Cells. 1126-1146
Volume 62, Number 5, March 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Raphaël Robidas, Claude Y. Legault:
CalcUS: An Open-Source Quantum Chemistry Web Platform. 1147-1153 - Alexander von Wedelstedt, Gunther Goebel, Grit Kalies:
MOF-VR: A Virtual Reality Program for Performing and Visualizing Immersive Molecular Dynamics Simulations of Guest Molecules in Metal-Organic Frameworks. 1154-1159 - Yuriy A. Abramov, Guangxu Sun, Qun Zeng:
Emerging Landscape of Computational Modeling in Pharmaceutical Development. 1160-1171 - Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot:
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. 1172-1177 - Kate A. Stafford, Brandon M. Anderson, Jon Sorenson, Henry van den Bedem:
AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens. 1178-1189 - Hyunsoo Park, Yeonghun Kang, Wonyoung Choe, Jihan Kim:
Mining Insights on Metal-Organic Framework Synthesis from Scientific Literature Texts. 1190-1198 - Michael Moret, Francesca Grisoni, Paul Katzberger, Gisbert Schneider:
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models. 1199-1206 - Taketomo Isazawa, Jacqueline M. Cole:
Single Model for Organic and Inorganic Chemical Named Entity Recognition in ChemDataExtractor. 1207-1213 - Jaime Carracedo-Cosme, Carlos Romero-Muñiz, Pablo Pou, Rubén Pérez:
QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy. 1214-1223 - Simon Cross, Gabriele Cruciani:
FragExplorer: GRID-Based Fragment Growing and Replacement. 1224-1235 - Luca Andrade, Aline Albuquerque, Andrielly Santos-Costa, Disraeli Vasconcelos, Wilson Savino, Geraldo Rodrigues Sartori, João Herminio Martins Da Silva:
Investigation of Unprecedented Sites and Proposition of New Ligands for Programmed Cell Death Protein I through Molecular Dynamics with Probes and Virtual Screening. 1236-1248 - Hongmao Sun, Nathan P. Coussens, Carina Danchik, Leah M. Wachsmuth, Mark J. Henderson, Samarjit Patnaik, Matthew D. Hall, Ashley L. Molinaro, Dayle A. Daines, Min Shen:
Discovery of Small-Molecule VapC1 Nuclease Inhibitors by Virtual Screening and Scaffold Hopping from an Atomic Structure Revealing Protein-Protein Interactions with a Native VapB1 Inhibitor. 1249-1258 - Javier L. Baylon, Oleg Ursu, Anja Muzdalo, Anne Mai Wassermann, Gregory L. Adams, Martin Spale, Petr Mejzlík, Anna Gromek, Viktor Pisarenko, Dzianis Hancharyk, Esteban Jenkins, David Bednar, Charlie Chang, Kamila Clarova, Meir Glick, Danny A. Bitton:
PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization. 1259-1267 - Alexander Zech, Timur Bazhirov:
CateCom: A Practical Data-Centric Approach to Categorization of Computational Models. 1268-1281 - Dharmeshkumar Patel, Stephanie L. Haag, Jagdish Suresh Patel, F. Marty Ytreberg, Matthew T. Bernards:
Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. 1282-1293 - Mohamed Marzouk Sobeh, Akio Kitao:
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM. 1294-1307 - Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang:
Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. 1308-1317 - Islem Hammami, Géraldine Farjot, Mikaël Naveau, Audrey Rousseaud, Thierry Prangé, Ira Katz, Nathalie Colloc'h:
Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families. 1318-1327 - Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi:
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease. 1328-1344 - Narod Kebabci, Ahmet Can Timucin, Emel Timuçin:
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment. 1345-1355
Volume 62, Number 6, March 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno:
AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge. 1357-1367 - Jinning Shao, Yue Liu, Jiaqi Yan, Ze-Yi Yan, Yangyang Wu, Zhongying Ru, Jia-Yu Liao, Xiaoye Miao, Linghui Qian:
Prediction of Maximum Absorption Wavelength Using Deep Neural Networks. 1368-1375 - Jieyu Lu, Yingkai Zhang:
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation. 1376-1387 - Giovanni Bolcato, Esther Heid, Jonas Boström:
On the Value of Using 3D Shape and Electrostatic Similarities in Deep Generative Methods. 1388-1398 - Chuan Li, Jiangting Liu, Jianfang Chen, Yuan Yuan, Jin Yu, Qiaolin Gou, Yanzhi Guo, Xuemei Pu:
An Interpretable Convolutional Neural Network Framework for Analyzing Molecular Dynamics Trajectories: a Case Study on Functional States for G-Protein-Coupled Receptors. 1399-1410 - Teresa Maria Creanza, Giuseppe Lamanna, Pietro Delre, Marialessandra Contino, Nicola Corriero, Michele Saviano, Giuseppe Felice Mangiatordi, Nicola Ancona:
DeLA-Drug: A Deep Learning Algorithm for Automated Design of Druglike Analogues. 1411-1424 - Corentin Bedart, Nicolas Renault, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, Monique Capron, Amaury Farce:
SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. 1425-1436 - Pradip Bera, Abhishek Aher, Paula Brandao, Utsab Debnath, Varun Dewaker, Sunil Kr. Manna, Abhimanyu Jana, Chandana Pramanik, Basudev Mandal, Pulakesh Bera:
Instigating the In Vitro Anticancer Activity of New Pyridine-Thiazole-Based Co(III), Mn(II), and Ni(II) Complexes: Synthesis, Structure, DFT, Docking, and MD Simulation Studies. 1437-1457 - Ellen E. Guest, Luis F. Cervantes, Stephen D. Pickett, Charles L. Brooks III, Jonathan D. Hirst:
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. 1458-1470 - Carlos E. S. Bernardes:
DLPGEN: Preparing Molecular Dynamics Simulations with Support for Polarizable Force Fields. 1471-1478 - Jonah Z. Vilseck, Luis F. Cervantes, Ryan L. Hayes, Charles L. Brooks III:
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. 1479-1488 - Noam Morningstar-Kywi, Kaichen Wang, Thomas R. Asbell, Zhaohui Wang, Jason B. Giles, Jiawei Lai, Dab Brill, Brian T. Sutch, Ian S. Haworth:
Prediction of Water Distributions and Displacement at Protein-Ligand Interfaces. 1489-1497 - Kowit Hengphasatporn, Patcharin Wilasluck, Peerapon Deetanya, Kittikhun Wangkanont, Warinthorn Chavasiri, Peerapat Visitchanakun, Asada Leelahavanichkul, Wattamon Paunrat, Siwaporn Boonyasuppayakorn, Thanyada Rungrotmongkol, Supot Hannongbua, Yasuteru Shigeta:
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease. 1498-1509 - Roberto López, Natalia Díaz, Evelio Francisco, Ángel Martín Pendás, Dimas Suárez:
QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. 1510-1524 - Steven R. Bowers, Dmitri K. Klimov, Christopher Lockhart:
Mechanisms of Binding of Antimicrobial Peptide PGLa to DMPC/DMPG Membrane. 1525-1537 - Alexander Neumann, Isaac Attah, Haneen Al-Hroub, Vigneshwaran Namasivayam, Christa E. Müller:
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening. 1538-1549 - C. Johan van der Westhuizen, André Stander, Darren L. Riley, Jenny-Lee Panayides:
Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations. 1550-1572 - Janez Konc, Samo Lesnik, Blaz Skrlj, Matej Sova, Matic Proj, Damijan Knez, Stanislav Gobec, Dusanka Janezic:
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. 1573-1584 - Amol Tagad, Reman Kumar Singh, G. Naresh Patwari:
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation. 1585-1594
Volume 62, Number 7, April 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Hugo Schweke, Marie-Hélène Mucchielli, Nicolas Chevrollier, Simon Gosset, Anne Lopes:
SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features. 1595-1601 - Amr H. Mahmoud, Matthew Masters, Soo Jung Lee, Markus A. Lill:
Accurate Sampling of Macromolecular Conformations Using Adaptive Deep Learning and Coarse-Grained Representation. 1602-1617 - Gonzalo Cerruela García, José Manuel Cuevas-Muñoz, Nicolás García-Pedrajas:
Graph-Based Feature Selection Approach for Molecular Activity Prediction. 1618-1632 - Miao Zhu, Jacqueline M. Cole:
PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format. 1633-1643 - Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey:
The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. 1644-1653 - Yi Hua, Xiaobao Fang, Guomeng Xing, Yuan Xu, Li Liang, Chenglong Deng, Xiaowen Dai, Haichun Liu, Tao Lu, Yanmin Zhang, Yadong Chen:
Effective Reaction-Based De Novo Strategy for Kinase Targets: A Case Study on MERTK Inhibitors. 1654-1668 - Bhagyesh Varvdekar, Akshay Prabhakant, Marimuthu Krishnan:
Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study. 1669-1679 - Bongkochawan Pakamwong, Paptawan Thongdee, Bundit Kamsri, Naruedon Phusi, Pharit Kamsri, Auradee Punkvang, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Kanchiyaphat Ariyachaokun, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, James Spencer, Adrian J. Mulholland, Pornpan Pungpo:
Identification of Potent DNA Gyrase Inhibitors Active against Mycobacterium tuberculosis. 1680-1690 - Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys:
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. 1691-1711 - Jiming Chen, David C. Nelson, Diwakar Shukla:
Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants. 1712-1722 - Osvaldo Burastero, Marisol Cabrera, Elias D. López, Lucas A. Defelipe, Juan Pablo Arcon, Rosario Durán, Marcelo A. Marti, Adrian Gustavo Turjanski:
Specificity and Reactivity of Mycobacterium tuberculosis Serine/Threonine Kinases PknG and PknB. 1723-1733 - Kang Ding, Shiqiu Yin, Zhongwei Li, Shiju Jiang, Yang Yang, Wenbiao Zhou, Yingsheng J. Zhang, Bo Huang:
Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research. 1734-1743 - Nabeel Ahmad, Anamika Singh, Akshita Gupta, Pradeep Pant, Tej P. Singh, Sujata Sharma, Pradeep Sharma:
Discovery of the Lead Molecules Targeting the First Step of the Histidine Biosynthesis Pathway of Acinetobacter baumannii. 1744-1759 - Huayuan Tang, Yunxiang Sun, Feng Ding:
Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation. 1760-1770 - Sungbo Hwang, Seung-Hwa Baek, Daeui Park:
Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. 1771-1782 - Anup P. Challa, Xin Hu, Ya-Qin Zhang, Jeffrey Hymes, Bret D. Wallace, Surendra Karavadhi, Hongmao Sun, Samarjit Patnaik, Matthew D. Hall, Min Shen:
Virtual Screening for the Discovery of Microbiome β-Glucuronidase Inhibitors to Alleviate Cancer Drug Toxicity. 1783-1793 - Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu:
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. 1794-1807
Volume 62, Number 8, April 2022
- Vineeth R. Chelur, U. Deva Priyakumar:
BiRDS - Binding Residue Detection from Protein Sequences Using Deep ResNets. 1809-1818 - Andrew T. McNutt, David Ryan Koes:
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. 1819-1829 - Xudong Zhang, Jun Mao, Min Wei, Yifei Qi, John Z. H. Zhang:
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models. 1830-1839 - Dongdong Zhang, Song Xia, Yingkai Zhang:
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning. 1840-1848 - Christophe Molina, Lilia Ait-Ouarab, Hervé Minoux:
Isometric Stratified Ensembles: A Partial and Incremental Adaptive Applicability Domain and Consensus-Based Classification Strategy for Highly Imbalanced Data Sets with Application to Colloidal Aggregation. 1849-1862 - Alba Fombona-Pascual, Javier Fombona, Rubén Vicente:
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures. 1863-1872 - Zhen Wang, Haitao Ji:
Characterization of Hydrophilic α-Helical Hot Spots on the Protein-Protein Interaction Interfaces for the Design of α-Helix Mimetics. 1873-1890 - She Zhang, Jeffrey P. Thompson, Junchao Xia, Anthony T. Bogetti, Forrest York, A. Geoffrey Skillman, Lillian T. Chong, David N. LeBard:
Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories. 1891-1904 - Pieter H. Bos, Evelyne M. Houang, Fabio Ranalli, Abba E. Leffler, Nicholas A. Boyles, Volker A. Eyrich, Yuval Luria, Dana Katz, Haifeng Tang, Robert Abel, Sathesh Bhat:
AutoDesigner, a De Novo Design Algorithm for Rapidly Exploring Large Chemical Space for Lead Optimization: Application to the Design and Synthesis of d-Amino Acid Oxidase Inhibitors. 1905-1915 - Srikanta Sen, Munna Sarkar:
Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study. 1916-1932 - Xiaoting Liu, Ji-Long Zhang:
In Silico Investigation on KAR Signaling Reveals the Significant Dynamic Change of Its Receptor's Structure. 1933-1941 - Souvik Mondal, Krishna Prasad Ghanta, Sanjoy Bandyopadhyay:
Dynamic Heterogeneity at the Interface of an Intrinsically Disordered Peptide. 1942-1955 - Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan:
Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. 1956-1978 - Phillip W. Gingrich, Justin B. Siegel, Dean J. Tantillo:
Assessing Alkene Reactivity toward Cytochrome P450-Mediated Epoxidation through Localized Descriptors and Regression Modeling. 1979-1987 - Peng Gao, Miao Xu, Qi Zhang, Catherine Z. Chen, Hui Guo, Yihong Ye, Wei Zheng, Min Shen:
Graph Convolutional Network-Based Screening Strategy for Rapid Identification of SARS-CoV-2 Cell-Entry Inhibitors. 1988-1997 - Juhi Dutta, Akshay Kumar Sahu, Abhijeet S. Bhadauria, Himansu S. Biswal:
Carbon-Centered Hydrogen Bonds in Proteins. 1998-2008
Volume 62, Number 9, May 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Matthias Rarey, Marc C. Nicklaus, Wendy A. Warr:
Special Issue on Reaction Informatics and Chemical Space. 2009-2010 - Pierre Baldi:
Call for a Public Open Database of All Chemical Reactions. 2011-2014 - Timur Gimadiev, Ramil I. Nugmanov, Aigul Khakimova, Adeliya Fatykhova, Timur I. Madzhidov, Pavel Sidorov, Alexandre Varnek:
CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. 2015-2020 - Wendy A. Warr, Marc C. Nicklaus, Christos A. Nicolaou, Matthias Rarey:
Exploration of Ultralarge Compound Collections for Drug Discovery. 2021-2034 - Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen, Regina Barzilay:
Automated Chemical Reaction Extraction from Scientific Literature. 2035-2045 - Vendy Fialková, Jiaxi Zhao, Kostas Papadopoulos, Ola Engkvist, Esben Jannik Bjerrum, Thierry Kogej, Atanas Patronov:
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design. 2046-2063 - Viraj Bagal, Rishal Aggarwal, P. K. Vinod, U. Deva Priyakumar:
MolGPT: Molecular Generation Using a Transformer-Decoder Model. 2064-2076 - Alexe L. Haywood, Joseph Redshaw, Magnus W. D. Hanson-Heine, Adam Taylor, Alex Brown, Andrew M. Mason, Thomas Gärtner, Jonathan D. Hirst:
Kernel Methods for Predicting Yields of Chemical Reactions. 2077-2092 - Rocío Mercado, Esben Jannik Bjerrum, Ola Engkvist:
Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation. 2093-2100 - Esther Heid, William H. Green Jr.:
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction. 2101-2110 - Philipp Seidl, Philipp Renz, Natalia Dyubankova, Paulo Neves, Jonas Verhoeven, Jörg K. Wegner, Marwin H. S. Segler, Sepp Hochreiter, Günter Klambauer:
Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks. 2111-2120 - Mohammadamin Tavakoli, Aaron Mood, David Van Vranken, Pierre Baldi:
Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity. 2121-2132 - Robert Schmidt, Raphael Klein, Matthias Rarey:
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. 2133-2150 - Yuliana Zabolotna, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin, Kostiantyn Gavrylenko, Dragos Horvath, Olga Klimchuk, Oleksandr Oksiuta, Gilles Marcou, Alexandre Varnek:
SynthI: A New Open-Source Tool for Synthon-Based Library Design. 2151-2163 - Peter Ertl:
Magic Rings: Navigation in the Ring Chemical Space Guided by the Bioactive Rings. 2164-2170 - Yuliana Zabolotna, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin, Dragos Horvath, Konstantin S. Gavrilenko, Gilles Marcou, Yurii S. Moroz, Oleksandr Oksiuta, Alexandre Varnek:
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. 2171-2185 - Timothy B. Dunn, Gustavo de M. Seabra, Taewon David Kim, K. Eurídice Juárez-Mercado, Chenglong Li, José L. Medina-Franco, Ramón Alain Miranda-Quintana:
Diversity and Chemical Library Networks of Large Data Sets. 2186-2201 - Joel Wahl, Thomas Sander:
Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib. 2202-2211 - Kazuma Kaitoh, Yoshihiro Yamanishi:
Scaffold-Retained Structure Generator to Exhaustively Create Molecules in an Arbitrary Chemical Space. 2212-2225 - Gergely Zahoránszky-Köhalmi, Nikita Lysov, Ilia Vorontcov, Jeffrey Wang, Jeyaraman Soundararajan, Dimitrios Metaxotos, Biju Mathew, Rafat Sarosh, Samuel G. Michael, Alexander G. Godfrey:
Algorithm for the Pruning of Synthesis Graphs. 2226-2238 - Hongyao Zhu, Timothy L. Foley, Justin I. Montgomery, Robert V. Stanton:
Understanding Data Noise and Uncertainty through Analysis of Replicate Samples in DNA-Encoded Library Selection. 2239-2247 - Dongming Lan, Shu Li, Wei Tang, Zexin Zhao, Mupeng Luo, Shuguang Yuan, Jun Xu, Yonghua Wang:
Glycerol is Released from a New Path in MGL Lipase Catalytic Process. 2248-2256
Volume 62, Number 10, May 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- Timothy Cholko, Shivansh Kaushik, Kingsley Y. Wu, Ruben Montes, Chia-en A. Chang:
GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems. 2257-2263 - Steven R. Shave, Nhan T. Pham, Manfred Auer:
CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens. 2264-2268 - Weixin Xie, Fanhao Wang, Yibo Li, Luhua Lai, Jianfeng Pei:
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models. 2269-2279 - Thomas E. Hadfield, Fergus Imrie, Andy Merritt, Kristian Birchall, Charlotte M. Deane:
Incorporating Target-Specific Pharmacophoric Information into Deep Generative Models for Fragment Elaboration. 2280-2292 - Cheng-Hao Liu, Maksym Korablyov, Stanislaw Jastrzebski, Pawel Wlodarczyk-Pruszynski, Yoshua Bengio, Marwin H. S. Segler:
RetroGNN: Fast Estimation of Synthesizability for Virtual Screening and De Novo Design by Learning from Slow Retrosynthesis Software. 2293-2300 - Heesung Shim, Hyojin Kim, Jonathan E. Allen, Heike Wulff:
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel-Ligand Docking. 2301-2315 - Katherine S. Lim, Andrew G. Reidenbach, Bruce K. Hua, Jeremy W. Mason, Christopher J. Gerry, Paul A. Clemons, Connor W. Coley:
Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function. 2316-2331 - Alexander P. Shevchenko, Michail I. Smolkov, Junjie Wang, Vladislav A. Blatov:
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds. 2332-2340 - Junhui Park, Gaeun Sung, Seunghyun Lee, Seungho Kang, Chunkyun Park:
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs. 2341-2351 - Lin Ji, Yue Li, Jie Wang, An Ning, Naixin Zhang, Shengyao Liang, Jiyun He, Tianyu Zhang, Zexing Qu, Jiali Gao:
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms. 2352-2364 - Thi Chinh Ngo, Duy Quang Dao, Tam Van-Thanh Mai, Thi Le Anh Nguyen, Lam Kim Huynh:
On The Radical Scavenging and DNA Repairing Activities by Natural Oxygenated Diterpenoids: Theoretical Insights. 2365-2377 - Dewi Yokelson, Nikolay V. Tkachenko, Robert Robey, Ying Wai Li, Pavel A. Dub:
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs. 2378-2386 - Narges Cheshmazar, Salar Hemmati, Maryam Hamzeh-Mivehroud, Babak Sokouti, Matthes Zessin, Mike Schutkowski, Wolfgang Sippl, Hojjatollah Nozad Charoudeh, Siavoush Dastmalchi:
Development of New Inhibitors of HDAC1-3 Enzymes Aided by In Silico Design Strategies. 2387-2397 - Wei-Hua Yang, Ya-Meng Li, Jian-Xiang Bi, Rao Huang, Gui-Fang Shao, Tian-E. Fan, Tun-Dong Liu, Yu-Hua Wen:
An Improved Self-Adaptive Differential Evolution with the Neighborhood Search Algorithm for Global Optimization of Bimetallic Clusters. 2398-2408 - Vikram Dalal, Dasantila Golemi-Kotra, Pravindra Kumar:
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. 2409-2420 - Xiu Li, Shiying Zhou, Xubo Lin:
Molecular View on the Impact of DHA Molecules on the Physical Properties of a Model Cell Membrane. 2421-2431 - Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud:
Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model. 2432-2445 - Valery R. Polyakov, Vadim Alexandrov, Andreas Maderna, Krishna Bajjuri, Xiaofan Li, Sihong Zhou:
Indexing Ultrafast Shape-Based Descriptors in MongoDB to Identify TLR4 Pathway Agonists. 2446-2455 - Sehr Naseem-Khan, Madison B. Berger, Emmett M. Leddin, Yazdan Maghsoud, G. Andrés Cisneros:
Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase. 2456-2465 - Leonardo F. Serafim, Vindi M. Jayasinghe-Arachchige, Lukun Wang, Rajeev Prabhakar:
Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. 2466-2480 - Carmen Domene, Leonardo Darré, Victoria Oakes, Saul Gonzalez-Resines:
A Potential Route of Capsaicin to Its Binding Site in the TRPV1 Ion Channel. 2481-2489 - Mert Golcuk, Aysima Hacisuleyman, Sema Zeynep Yilmaz, Elhan Taka, Ahmet Yildiz, Mert Gur:
SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity. 2490-2498 - Xiaolin Pan, Hao Wang, Yueqing Zhang, Xingyu Wang, Cuiyu Li, Changge Ji, John Z. H. Zhang:
AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. 2499-2509 - Luís M. C. Teixeira, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes:
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic. 2510-2521 - Sukanya Mozumder, Aritra Bej, Jayati Sengupta:
Ligand-Dependent Modulation of the Dynamics of Intracellular Loops Dictates Functional Selectivity of 5-HT2AR. 2522-2537 - Qiaojing Huang, Luhua Lai, Zhirong Liu:
Quantitative Analysis of Dynamic Allostery. 2538-2549 - Nuno F. B. Oliveira, Miguel Machuqueiro:
Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. 2550-2560 - Shunzhou Wan, Agastya P. Bhati, David W. Wright, Ian D. Wall, Alan P. Graves, Darren V. S. Green, Peter V. Coveney:
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. 2561-2570 - Nemanja Djokovic, Dusan Ruzic, Minna Rahnasto-Rilla, Tatjana Srdic-Rajic, Maija Lahtela-Kakkonen, Katarina Nikolic:
Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics. 2571-2585 - Xavier Chee Wezen, Aneesh Chandran, Rohan Sakariah Eapen, Elaine Waters, Laura Bricio-Moreno, Tommaso Tosi, Stephen Dolan, Charlotte Millership, Aras Kadioglu, Angelika Gründling, Laura S. Itzhaki, Martin Welch, Taufiq Rahman:
Structure-Based Discovery of Lipoteichoic Acid Synthase Inhibitors. 2586-2599 - Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann, Andrea Volkamer:
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. 2600-2616 - Qushuo Chen, Changyan Yang, Yihao Xie, Yuqiang Wang, Xiaoxu Li, Kairong Wang, Jinqi Huang, Wenjin Yan:
GM-Pep: A High Efficiency Strategy to De Novo Design Functional Peptide Sequences. 2617-2629
Volume 62, Number 11, June 2022
- Fiorella Ruggiu, Caitlin C. Bannan, Andrea N. Bootsma:
Early Career Perspectives from Large Pharma, Software, and Start-up Companies. 2631-2638 - Maciej Spiegel:
Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity. 2639-2658 - Yuhong Wang, Samuel G. Michael, Shyh-Ming Yang, Ruili Huang, Kennie Cruz-Gutierrez, Yaqing Zhang, Jinghua Zhao, Menghang Xia, Paul Shinn, Hongmao Sun:
Retro Drug Design: From Target Properties to Molecular Structures. 2659-2669 - Jiuyang Zhao, Jacqueline M. Cole:
Reconstructing Chromatic-Dispersion Relations and Predicting Refractive Indices Using Text Mining and Machine Learning. 2670-2684 - Navneet Bung, Sowmya Ramaswamy Krishnan, Arijit Roy:
An In Silico Explainable Multiparameter Optimization Approach for De Novo Drug Design against Proteins from the Central Nervous System. 2685-2695 - Chao Yang, Yingkai Zhang:
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. 2696-2712 - Yuyang Wang, Rishikesh Magar, Chen Liang, Amir Barati Farimani:
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast. 2713-2725 - Michael C. Hutter:
Differential Multimolecule Fingerprint for Similarity Search─Making Use of Active and Inactive Compound Sets in Virtual Screening. 2726-2736 - Andrea Jacobs, Dustin Williams, Katherine Hickey, Nathan Patrick, Antony J. Williams, Stuart J. Chalk, Leah McEwen, Egon L. Willighagen, Martin Walker, Evan Bolton, Gabriel Sinclair, Adam Sanford:
CAS Common Chemistry in 2021: Expanding Access to Trusted Chemical Information for the Scientific Community. 2737-2743 - Xiang Cai, Wei Han:
Development of a Hybrid-Resolution Force Field for Peptide Self-Assembly Simulations: Optimizing Peptide-Peptide and Peptide-Solvent Interactions. 2744-2760 - Sinan Kardas, Mathieu Fossépré, Vincent Lemaur, Antony E. Fernandes, Karine Glinel, Alain M. Jonas, Mathieu Surin:
Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis. 2761-2770 - Francesca Galvani, Laura Scalvini, Silvia Rivara, Alessio Lodola, Marco Mor:
Mechanistic Modeling of Monoglyceride Lipase Covalent Modification Elucidates the Role of Leaving Group Expulsion and Discriminates Inhibitors with High and Low Potency. 2771-2787 - Chaofeng Lou, Hongbin Yang, Jiye Wang, Mengting Huang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method. 2788-2799 - Louis Bellmann, Raphael Klein, Matthias Rarey:
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. 2800-2810 - Adrien Varet, Nicolas Prcovic, Cyril Terrioux, Denis Hagebaum-Reignier, Yannick Carissan:
BenzAI: A Program to Design Benzenoids with Defined Properties Using Constraint Programming. 2811-2820 - Abdul Basit, Ajeet Kumar Yadav, Pradipta Bandyopadhyay:
Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. 2821-2834 - Xu Yan, Yingfeng Lu, Zhen Li, Qing Wei, Xin Gao, Sheng Wang, Song Wu, Shuguang Cui:
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms. 2835-2845 - Hiraku Oshima, Yuji Sugita:
Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions. 2846-2856 - José X. Lima Neto, Davi S. Vieira, Jones de Andrade, Umberto Laino Fulco:
Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63. 2857-2868 - Xiyu Chen, Sigrid Leyendecker, Henry van den Bedem:
Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. 2869-2879 - Lijuan Yan, Yongjun Liu:
Mechanistic Insights into the Anaerobic Degradation of Globally Abundant Dihydroxypropanesulfonate Catalyzed by the DHPS-Sulfolyase (HpsG). 2880-2888 - Norio Yoshida, Yutaka Maruyama, Ayori Mitsutake, Akiyoshi Kuroda, Ryo Fujiki, Kodai Kanemaru, Daisuke Okamoto, Alexander E. Kobryn, Sergey Gusarov, Haruyuki Nakano:
Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory. 2889-2898
Volume 62, Number 12, June 2022
- Issue Editorial Masthead.
- Issue Publication Information.
- Lydia Siragusa, Gabriele Menna, Fabrizio Buratta, Massimo Baroni, Jenny Desantis, Gabriele Cruciani, Laura Goracci:
CROMATIC: Cross-Relationship Map of Cavities from Coronaviruses. 2901-2908 - Genki Imam Prayogo, Andrea Tirelli, Keishu Utimula, Kenta Hongo, Ryo Maezono, Kousuke Nakano:
Shry: Application of Canonical Augmentation to the Atomic Substitution Problem. 2909-2915 - Hao Wang, Xiaolin Pan, Yueqing Zhang, Xingyu Wang, Xudong Xiao, Changge Ji:
MolHyb: A Web Server for Structure-Based Drug Design by Molecular Hybridization. 2916-2922 - Huaipan Jiang, Jian Wang, Weilin Cong, Yihe Huang, Morteza Ramezani, Anup Sarma, Nikolay V. Dokholyan, Mehrdad Mahdavi, Mahmut T. Kandemir:
Predicting Protein-Ligand Docking Structure with Graph Neural Network. 2923-2932 - Joonyoung F. Joung, Minhi Han, Minseok Jeong, Sungnam Park:
Beyond Woodward-Fieser Rules: Design Principles of Property-Oriented Chromophores Based on Explainable Deep Learning Optical Spectroscopy. 2933-2942 - Myeonghun Lee, Kyoungmin Min:
MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder. 2943-2950 - Vincenzo Laveglia, Andrea Giachetti, Davide Sala, Claudia Andreini, Antonio Rosato:
Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. 2951-2960 - Erik Otovic, Marko Njirjak, Daniela Kalafatovic, Goran Mausa:
Sequential Properties Representation Scheme for Recurrent Neural Network-Based Prediction of Therapeutic Peptides. 2961-2972 - Jiahui Yu, Jike Wang, Hong Zhao, Junbo Gao, Yu Kang, Dong-Sheng Cao, Zhe Wang, Tingjun Hou:
Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. 2973-2986 - Denis N. Prada Gori, Manuel A. Llanos, Carolina L. Bellera, Alan Talevi, Lucas N. Alberca:
iRaPCA and SOMoC: Development and Validation of Web Applications for New Approaches for the Clustering of Small Molecules. 2987-2998 - Kosala Amarasinghe, Leonardo De Maria, Christian Tyrchan, Leif A. Eriksson, Jens Sadowski, Dusan Petrovic:
Virtual Screening Expands the Non-Natural Amino Acid Palette for Peptide Optimization. 2999-3007 - Manuel A. Llanos, Nicolas Enrique, María L. Sbaraglini, Federico M. Garofalo, Alan Talevi, Luciana Gavernet, Pedro Martín:
Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo. 3008-3022 - Maria Antonietta La Serra, Pietro Vidossich, Isabella Acquistapace, Anand K. Ganesan, Marco de Vivo:
Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex. 3023-3033 - Pedro R. Magalhães, Pedro B. P. S. Reis, Diogo Vila-Viçosa, Miguel Machuqueiro, Bruno L. Victor:
Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds. 3034-3042 - Salomé Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emília P. Barros, Philippe H. Hünenberger, Sereina Riniker:
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. 3043-3056 - Minjie Kang, Zhicheng Zuo, Zhixiang Yin, Jianrong Gu:
Molecular Mechanism of D1135E-Induced Discriminated CRISPR-Cas9 PAM Recognition. 3057-3066 - Daniel Bustos, Erix Wiliam Hernández-Rodríguez, Horacio Poblete, Jans H. Alzate-Morales, Cecilia Challier, Cristhian Boetsch, Ariela Vergara Jaque, Paola Beassoni:
Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa. 3067-3078 - Adan Gallardo, Brandon M. Bogart, Bercem Dutagaci:
Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations. 3079-3089 - Xueying Wang, Shuguang Yuan, H. C. Stephen Chan:
Translocation Mechanism of Allosteric Sodium Ions in β2-Adrenoceptor. 3090-3095 - Jeremy Morere, Cécilia Hognon, Tom Miclot, Tao Jiang, Elise Dumont, Giampaolo Barone, Antonio Monari, Emmanuelle Bignon:
How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency. 3096-3106 - Aria Gheeraert, Laurent Vuillon, Laurent Chaloin, Olivier Moncorgé, Thibaut Very, Serge Perez, Vincent Leroux, Isaure Chauvot de Beauchêne, Dominique Mias-Lucquin, Marie-Dominique Devignes, Ivan Rivalta, Bernard Maigret:
Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis. 3107-3122 - Yongjun Zang, Luyang Tai, Yuanyang Hu, Yu Wang, Hongbin Sun, Xiaoan Wen, Haoliang Yuan, Liang Dai:
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor. 3123-3132
Volume 62, Number 13, July 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Giulia Palermo:
Celebrating Women of Color in Computational Chemistry. 3133-3134 - Reagan J. Meredith, Luke Sernau, Anthony S. Serianni:
MA'AT: A Web-Based Application to Determine Rotamer Population Distributions in Solution from Nuclear Magnetic Resonance Spin-Coupling Constants. 3135-3141 - Michael Schauperl, Rajiah Aldrin Denny:
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges. 3142-3156 - Sangwoo Park, Chaok Seok:
GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. 3157-3168 - Alexis W. Mills, Joshua J. Goings, David Beck, Chao Yang, Xiaosong Li:
Exploring Potential Energy Surfaces Using Reinforcement Machine Learning. 3169-3179 - Seid Hamzic, Richard A. Lewis, Sandrine Desrayaud, Cihan Soylu, Mike Fortunato, Grégori Gerebtzoff, Raquel Rodríguez-Pérez:
Predicting In Vivo Compound Brain Penetration Using Multi-task Graph Neural Networks. 3180-3190 - Yuwei Yang, Zhenxing Wu, Xiaojun Yao, Yu Kang, Tingjun Hou, Chang-Yu Hsieh, Huanxiang Liu:
Exploring Low-Toxicity Chemical Space with Deep Learning for Molecular Generation. 3191-3199 - Manuel A. Llanos, Clara Ventura, Pedro Martín, Nicolas Enrique, Juan I. Felice, Luciana Gavernet, Verónica Milesi:
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect. 3200-3212 - Lingyan Wang, Kun Xi, Lizhe Zhu, Lin-Tai Da:
DNA Deformation Exerted by Regulatory DNA-Binding Motifs in Human Alkyladenine DNA Glycosylase Promotes Base Flipping. 3213-3226 - Zenghui Lao, Xuewei Dong, Xianshi Liu, Fangying Li, Yujie Chen, Yiming Tang, Guanghong Wei:
Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain. 3227-3238 - Abdelazim M. A. Abdelgawwad, Antonio Monari, Iñaki Tuñón, Antonio Francés-Monerris:
Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative. 3239-3252 - Lane W. Votapka, Andrew M. Stokely, Anupam Anand Ojha, Rommie E. Amaro:
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. 3253-3262 - Raitis Bobrovs, Emils Edgars Basens, Laura Drunka, Iveta Kanepe, Sofija Matisone, Karlis Kristofers Velins, Victor Andrianov, Gundars Leitis, Diana Zelencova-Gopejenko, Dace Rasina, Aigars Jirgensons, Kristaps Jaudzems:
Exploring Aspartic Protease Inhibitor Binding to Design Selective Antimalarials. 3263-3273
Volume 62, Number 14, July 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Robert P. Sheridan, J. Christopher Culberson, Elizabeth Joshi, Matthew Tudor, Prabha Karnachi:
Prediction Accuracy of Production ADMET Models as a Function of Version: Activity Cliffs Rule. 3275-3280 - Cunxing Lu, Xili Wan, Xuhao Ma, Xinjie Guan, Aichun Zhu:
Deep-Learning-Based End-to-End Predictions of CO2 Capture in Metal-Organic Frameworks. 3281-3290 - Jie Zhang, Hongming Chen:
De Novo Molecule Design Using Molecular Generative Models Constrained by Ligand-Protein Interactions. 3291-3306 - Ramil I. Nugmanov, Natalia Dyubankova, Andrey Gedich, Jörg Kurt Wegner:
Bidirectional Graphormer for Reactivity Understanding: Neural Network Trained to Reaction Atom-to-Atom Mapping Task. 3307-3315 - Yue Zhang, Cong Wang, Mya Soukaseum, Dionisios G. Vlachos, Hui Fang:
Unleashing the Power of Knowledge Extraction from Scientific Literature in Catalysis. 3316-3330 - Fei Zhu, Sijie Yang, Fanwang Meng, Yuxiang Zheng, Xin Ku, Cheng Luo, Guang Hu, Zhongjie Liang:
Leveraging Protein Dynamics to Identify Functional Phosphorylation Sites using Deep Learning Models. 3331-3345 - Beibei Wang, Shane Jackson, Aiichiro Nakano, Ken-ichi Nomura, Priya Vashishta, Rajiv K. Kalia, Mark Stevens:
Neural Network for Principle of Least Action. 3346-3351 - Atsushi Tokuhisa, Yoshinobu Akinaga, Kei Terayama, Yuji Okamoto, Yasushi Okuno:
Single-Image Super-Resolution Improvement of X-ray Single-Particle Diffraction Images Using a Convolutional Neural Network. 3352-3364 - Jesús Lucia-Tamudo, Gustavo Cárdenas, Nuria Anguita-Ortiz, Sergio Díaz-Tendero, Juan J. Nogueira:
Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches. 3365-3380 - Amit Kumar, Harish Vashisth:
Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides. 3381-3390 - Kristoffer T. Bæk, Kasper P. Kepp:
Assessment of AlphaFold2 for Human Proteins via Residue Solvent Exposure. 3391-3400 - Marko Hanzevacki, Anna K. Croft, Christof M. Jäger:
Activation of Glycyl Radical Enzymes─Multiscale Modeling Insights into Catalysis and Radical Control in a Pyruvate Formate-Lyase-Activating Enzyme. 3401-3414 - Anita Rácz, Levente M. Mihalovits, Dávid Bajusz, Károly Héberger, Ramón Alain Miranda-Quintana:
Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices. 3415-3425 - Maximilian Meixner, Martin Zachmann, Sebastian Metzler, Jonathan Scheerer, Martin Zacharias, Iris Antes:
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock. 3426-3441 - Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins. 3442-3452 - Prabir Khatua, Madhulika Gupta, Sanjoy Bandyopadhyay:
Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations. 3453-3462 - Hatice Gokcan, Jirair K. Bedoyan, Olexandr Isayev:
Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. 3463-3475
Volume 62, Number 15, August 2022
- Robert P. Sheridan:
Stability of Prediction in Production ADMET Models as a Function of Version: Why and When Predictions Change. 3477-3485 - Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp, José Miguel Hernández-Lobato, Andreas Bender, Sergio Bacallado:
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design. 3486-3502 - Zhengkai Tu, Connor W. Coley:
Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction. 3503-3513 - Abdulmohsen A. Alsaui, Yousef A. Alghofaili, Mohammed Alghadeer, Fahhad H. Alharbi:
Resampling Techniques for Materials Informatics: Limitations in Crystal Point Groups Classification. 3514-3523 - Tagir Akhmetshin, Arkadii I. Lin, Daniyar Mazitov, Yuliana Zabolotna, Evgenii Ziaikin, Timur I. Madzhidov, Alexandre Varnek:
HyFactor: A Novel Open-Source, Graph-Based Architecture for Chemical Structure Generation. 3524-3534 - Natália Aniceto, Vasco D. B. Bonifácio, Rita C. Guedes, Nuno Martinho:
Exploring the Chemical Space of Urease Inhibitors to Extract Meaningful Trends and Drivers of Activity. 3535-3550 - Vincent Blay, Tijana Radivojevic, Jonathan E. Allen, Corey M. Hudson, Héctor García Martín:
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design. 3551-3564 - Uschi Dolfus, Hans Briem, Matthias Rarey:
Synthesis-Aware Generation of Structural Analogues. 3565-3576 - Gonzalo F. Mayol, Lucas A. Defelipe, Juan Pablo Arcon, Adrian Gustavo Turjanski, Marcelo A. Marti:
Solvent Sites Improve Docking Performance of Protein-Protein Complexes and Protein-Protein Interface-Targeted Drugs. 3577-3588 - Bregje W. Brinkmann, Ankush Singhal, G. J. Agur Sevink, Lisette Neeft, Martina G. Vijver, Willie J. G. M. Peijnenburg:
Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials. 3589-3603 - Walter Fiedler, Fabian Freisleben, Jasmin Wellbrock, Karl N. Kirschner:
Mebendazole's Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90. 3604-3617 - Pedro A. Valiente, Satra Nim, Jinah Lee, Seungtaek Kim, Philip M. Kim:
Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern. 3618-3626 - Shih-Hsien Liu, Zhousheng Xiao, Sambit K. Mishra, Julie C. Mitchell, Jeremy C. Smith, L. Darryl Quarles, Loukas Petridis:
Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho. 3627-3637 - Rui P. P. Neves, Pedro Alexandrino Fernandes, Maria João Ramos:
Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. 3638-3650 - Tao Jiang, Zhenhao Liu, Wenlang Liu, Jiawen Chen, Zheng Zheng, Mojie Duan:
The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations. 3651-3663 - Dan Teng, Yang Zhou, Yun Tang, Guixia Liu, Yaoquan Tu:
Mechanistic Studies on the Stereoselectivity of FFAR1 Modulators. 3664-3675 - Jingjing Zheng, Yurong Qian, Jie He, Zerui Kang, Lei Deng:
Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. 3676-3684
Volume 62, Number 16, August 2022
- Filipe Menezes, Grzegorz M. Popowicz:
ULYSSES: An Efficient and Easy to Use Semiempirical Library for C++. 3685-3694 - Chaoshu Duan, Xuyang Liu, Wensheng Cai, Xueguang Shao:
Spectral Encoder to Extract the Features of Near-Infrared Spectra for Multivariate Calibration. 3695-3703 - Alexandra Wahab, Lara Pfuderer, Eno Paenurk, Renana Gershoni-Poranne:
The COMPAS Project: A Computational Database of Polycyclic Aromatic Systems. Phase 1: cata-Condensed Polybenzenoid Hydrocarbons. 3704-3713 - Florian Spenke, Bernd Hartke:
Graph-based Automated Macro-Molecule Assembly. 3714-3723 - Ethan King, Richard Overstreet, Julia Nguyen, Danielle Ciesielski:
Augmentation of MS/MS Libraries with Spectral Interpolation for Improved Identification. 3724-3733 - Andrés Sánchez-Ruiz, Gonzalo Colmenarejo:
Systematic Analysis and Prediction of the Target Space of Bioactive Food Compounds: Filling the Chemobiological Gaps. 3734-3751 - Kunal Kumar Jha, Barbara Gruza, Aleksandra Sypko, Prashant Kumar, Michal Chodkiewicz, Paulina Maria Dominiak:
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB. 3752-3765 - Paulina Maria Rybicka, Marta Kulik, Michal Chodkiewicz, Paulina Maria Dominiak:
Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis. 3766-3783 - Stefania Monteleone, Dmitri G. Fedorov, Andrea Townsend-Nicholson, Michelle Southey, Michael J. Bodkin, Alexander Heifetz:
Hotspot Identification and Drug Design of Protein-Protein Interaction Modulators Using the Fragment Molecular Orbital Method. 3784-3799 - Nisha Amarnath Jonniya, Parimal Kar:
Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. 3800-3813 - Mehdi Sahihi, Jordi Faraudo:
Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface. 3814-3824 - Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell Jr.:
Preserving the Integrity of Empirical Force Fields. 3825-3831 - Dusan Petrovic, James S. Scott, Michael S. Bodnarchuk, Olivier Lorthioir, Scott Boyd, George M. Hughes, Jordan Lane, Allan Wu, David Hargreaves, James Robinson, Jens Sadowski:
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors. 3832-3843 - Zsolt Fazekas, Dóra K. Menyhárd, András Perczel:
Omicron Binding Mode: Contact Analysis and Dynamics of the Omicron Receptor-Binding Domain in Complex with ACE2. 3844-3853 - David E. Graff, Matteo Aldeghi, Joseph A. Morrone, Kirk E. Jordan, Edward O. Pyzer-Knapp, Connor W. Coley:
Self-Focusing Virtual Screening with Active Design Space Pruning. 3854-3862 - Han Liu, Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai:
Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. 3863-3873 - Nicole Balasco, Antonella Paladino, Giuseppe Graziano, Marco D'Abramo, Luigi Vitagliano:
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs. 3874-3884 - Viet Hoang Man, Xibing He, Junmei Wang:
Stable Cavitation Interferes with Aβ16-22 Oligomerization. 3885-3895 - Mitja Ogrizek, Matej Janezic, Katja Valjavec, Andrej Perdih:
Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα. 3896-3909 - Rino Ragno, Anna Minarini, Eleonora Proia, Lorenzo Antonini, Andrea Milelli, Vincenzo Tumiatti, Marco Fiore, Pasquale Fino, Lavinia Rutigliano, Rossella Fioravanti, Tomoaki Tahara, Elena Pacella, Antonio Greco, Gianluca Canettieri, Maria Luisa Di Paolo, Enzo Agostinelli:
Bovine Serum Amine Oxidase and Polyamine Analogues: Chemical Synthesis and Biological Evaluation Integrated with Molecular Docking and 3-D QSAR Studies. 3910-3927 - Carlos Santiago, Bernabé Ortega-Tenezaca, Iratxe Barbolla, Brenda Fundora-Ortiz, Sonia Arrasate, María Auxiliadora Dea-Ayuela, Humberto González Díaz, Nuria Sotomayor, Esther Lete:
Prediction of Antileishmanial Compounds: General Model, Preparation, and Evaluation of 2-Acylpyrrole Derivatives. 3928-3940
Volume 62, Number 17, September 2022
- Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.:
Editorial on Machine Learning. 3941 - Thomas Fox, Michael Bieler, Peter Haebel, Rodrigo Ochoa, Stefan Peters, Alexander Weber:
BILN: A Human-Readable Line Notation for Complex Peptides. 3942-3947 - Gabriel A. Pinheiro, Juarez L. F. Da Silva, Marcos G. Quiles:
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning. 3948-3960 - Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia:
Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation. 3961-3969 - Hugo Bellamy, Abbi Abdel-Rehim, Oghenejokpeme I. Orhobor, Ross D. King:
Batched Bayesian Optimization for Drug Design in Noisy Environments. 3970-3981 - Katsuhisa Morita, Tadahaya Mizuno, Hiroyuki Kusuhara:
Investigation of a Data Split Strategy Involving the Time Axis in Adverse Event Prediction Using Machine Learning. 3982-3992 - Qinghua Wang, Zhe Wang, Sheng Tian, Lingling Wang, Rongfan Tang, Yang Yu, Jingxuan Ge, Tingjun Hou, Haiping Hao, Huiyong Sun:
Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. 3993-4007 - Wenjian Ma, Shugang Zhang, Zhen Li, Mingjian Jiang, Shuang Wang, Weigang Lu, Xiangpeng Bi, Huasen Jiang, Henggui Zhang, Zhiqiang Wei:
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures. 4008-4017 - Gulnara Shavalieva, Stavros Papadokonstantakis, Gregory Peters:
Prior Knowledge for Predictive Modeling: The Case of Acute Aquatic Toxicity. 4018-4031 - Ryuichiro Ishitani, Toshiki Kataoka, Kentaro Rikimaru:
Molecular Design Method Using a Reversible Tree Representation of Chemical Compounds and Deep Reinforcement Learning. 4032-4048 - Parker Ladd Bremer, Arpana Vaniya, Tobias Kind, Shunyang Wang, Oliver Fiehn:
How Well Can We Predict Mass Spectra from Structures? Benchmarking Competitive Fragmentation Modeling for Metabolite Identification on Untrained Tandem Mass Spectra. 4049-4056 - Hiroaki Iwata, Tatsuru Matsuo, Hideaki Mamada, Takahisa Motomura, Mayumi Matsushita, Takeshi Fujiwara, Kazuya Maeda, Koichi Handa:
Predicting Total Drug Clearance and Volumes of Distribution Using the Machine Learning-Mediated Multimodal Method through the Imputation of Various Nonclinical Data. 4057-4065 - Justin Legleiter, Ravindra Thakkar, Astrid Velásquez-Silva, Ingrid Miranda-Carvajal, Susan Whitaker, John Tomich, Jeffrey Comer:
Design of Peptides that Fold and Self-Assemble on Graphite. 4066-4082 - Alberto M. dos Santos, Amanda Ruslana Santana Oliveira, Clauber Henrique Costa, Peter W. Kenny, Carlos Alberto Montanari, Jaldyr de Jesus G. Varela, Jerônimo Lameira:
Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces. 4083-4094 - Ebru Akkus, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak:
Accurate Binding Free Energy Method from End-State MD Simulations. 4095-4106 - Emilian Tuca, Gino Dilabio, Alberto Otero-de-la-Roza:
Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction. 4107-4121 - Yongna Yuan, Haoqiu Yan, Zeyang Cui, Zhenyu Liu, Wei Su, Ruisheng Zhang:
Quantum Chemical Calculations with Machine Learning for Multipolar Electrostatics Prediction in RNA: An Application to Pentose. 4122-4133 - Elisabeth Kallert, Tim R. Fischer, Simon Schneider, Maike Grimm, Mark Helm, Christian Kersten:
Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch. 4134-4148 - Evan Gildernew, Sungwoo Yang:
Finite Element Modeling of Atmospheric Water Extraction by Way of Highly Porous Adsorbents: A Roadmap for Solver Construction with Model Factor Sensitivity Screening. 4149-4161 - Duván González, Luis Macaya, Carlos Castillo-Orellana, Toon Verstraelen, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez:
Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions. 4162-4174 - Iris N. Smith, Jennifer E. Dawson, James Krieger, Stetson Thacker, Ivet Bahar, Charis Eng:
Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation. 4175-4190 - K. Michael Salerno, Janna Domenico, Nam Q. Le, Christopher D. Stiles, Ilia A. Solov'yov, Carlos F. Martino:
Long-Time Oxygen Localization in Electron Transfer Flavoprotein. 4191-4199 - Lukas Schulig, Norman Geist, Mihaela Delcea, Andreas Link, Martin Kulke:
Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity. 4200-4209 - Bin Sun, Peter M. Kekenes-Huskey:
Calmodulin's Interdomain Linker Is Optimized for Dynamics Signal Transmission and Calcium Binding. 4210-4221 - Hao Zhang, Duan Ni, Jigang Fan, Minyu Li, Jian Zhang, Chen Hua, Ruth Nussinov, Shaoyong Lu:
Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. 4222-4231 - Osita Sunday Nnyigide, Tochukwu Olunna Nnyigide, Sun-Gu Lee, Kyu Hyun:
Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions. 4232-4246 - Sayyed Jalil Mahdizadeh, Emil Pålsson, Antonio Carlesso, Eric Chevet, Leif A. Eriksson:
QM/MM Well-Tempered Metadynamics Study of the Mechanism of XBP1 mRNA Cleavage by Inositol Requiring Enzyme 1α RNase. 4247-4260 - Emmanuelle Bignon, Antonio Monari:
Modeling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent RNA Polymerase by DFT/MM-MD: An Unusual Active Site Leading to High Replication Rates. 4261-4269 - Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song:
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. 4270-4282 - Guan-Yu Zhu, Yan Liu, Peng-Hao Wang, Xibei Yang, Dong-Jun Yu:
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning. 4283-4291 - Giulia Palermo:
Celebrating the Next Generation of Women in Computational Chemistry to Increase Diversity, Equity, Inclusion, and Respect. 4292-4293
Volume 62, Number 18, September 2022
- Jannis Born, Yoel Shoshan, Tien Huynh, Wendy D. Cornell, Eric J. Martin, Matteo Manica:
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction. 4295-4299 - Alexandre V. Fassio, Laura Shub, Luca Ponzoni, Jessica McKinley, Matthew J. O'Meara, Rafaela Salgado Ferreira, Michael J. Keiser, Raquel Cardoso de Melo Minardi:
Prioritizing Virtual Screening with Interpretable Interaction Fingerprints. 4300-4318 - Wan Nie, Deguang Liu, Shuaicheng Li, Haizhu Yu, Yao Fu:
Nucleophilicity Prediction Using Graph Neural Networks. 4319-4328 - Md. Masud Rana, Duc Duy Nguyen:
EISA-Score: Element Interactive Surface Area Score for Protein-Ligand Binding Affinity Prediction. 4329-4341 - Madeleine D. Breshears, Rajiv Giridharagopal, Justin Pothoof, David S. Ginger:
A Robust Neural Network for Extracting Dynamics from Electrostatic Force Microscopy Data. 4342-4350 - Thijs Beuming, Helena Martín, Anna M. Díaz-Rovira, Lucía Díaz, Victor Guallar, Soumya S. Ray:
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. 4351-4360 - Xue Zong, Dionisios G. Vlachos:
Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning. 4361-4368 - Xiaoyang Qu, Lina Dong, Jinyan Zhang, Yubing Si, Binju Wang:
Systematic Improvement of the Performance of Machine Learning Scoring Functions by Incorporating Features of Protein-Bound Water Molecules. 4369-4379 - Qingyu Li, Xiaochang Zhang, Lianlian Wu, Xiaochen Bo, Song He, Shengqi Wang:
PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations. 4380-4390 - Daniel J. Woodward, Anthony R. Bradley, Willem P. van Hoorn:
Coverage Score: A Model Agnostic Method to Efficiently Explore Chemical Space. 4391-4402 - Shunyang Wang, Tobias Kind, Parker Ladd Bremer, Dean J. Tantillo, Oliver Fiehn:
Beyond the Ground State: Predicting Electron Ionization Mass Spectra Using Excited-State Molecular Dynamics. 4403-4410 - Mohamed Korany, Ida Ritacco, Eslam Dabbish, Emilia Sicilia, Tamer Shoeib:
Analysis of the Fragmentation Pathways for the Collision-Induced Dissociation of Protonated Cyclophosphamide: A Mass Spectrometry and Quantum Mechanical Study. 4411-4419 - Liming Zhao, Mengchen Pu, Huting Wang, Xiangyu Ma, Yingsheng J. Zhang:
Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design. 4420-4426 - Masato Sumita, Kei Terayama, Ryo Tamura, Koji Tsuda:
QCforever: A Quantum Chemistry Wrapper for Everyone to Use in Black-Box Optimization. 4427-4434 - António M. Baptista, Lucie da Rocha, Sara R. R. Campos:
FixBox: A General Algorithm to Fix Molecular Systems in Periodic Boxes. 4435-4447 - Yuan Hu, Ingo Muegge:
In Silico Positional Analogue Scanning with Amber GPU-TI. 4448-4459 - Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta, Takashi Yoshidome:
gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins. 4460-4473 - Azamat Rizuan, Nina Jovic, Tien M. Phan, Young C. Kim, Jeetain Mittal:
Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. 4474-4485 - Rachel T. Payne, Silvia Crivelli, Masakatsu Watanabe:
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System. 4486-4499 - Taeho Kim, Kewon Kim, Inyoung Park, Sungwoo Hong, Hwangseo Park:
Two-Track Virtual Screening Approach to Identify the Dual Inhibitors of Wild Type and C481S Mutant of Bruton's Tyrosine Kinase. 4500-4511 - Liping Zhou, Tingting Liu, Mengxia Mo, Yulong Shi, Leyun Wu, Yishui Li, Qiuping Qin, Weiliang Zhu, Chengkun Wu, Likun Gong, Zhijian Xu:
Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay. 4512-4522 - Yumeng Zhang, Xiaorong Liu, Jianhan Chen:
Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. 4523-4536 - Yuliana Zabolotna, Fanny Bonachéra, Dragos Horvath, Arkadii I. Lin, Gilles Marcou, Olga Klimchuk, Alexandre Varnek:
Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery. 4537-4548 - Masatake Sugita, Takuya Fujie, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama:
Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. 4549-4560 - José Ramón López-Blanco, Yves Dehouck, Ugo Bastolla, Pablo Chacón:
Local Normal Mode Analysis for Fast Loop Conformational Sampling. 4561-4568
Volume 62, Number 19, October 2022
- Thanh T. Lai, David M. Kuntz, Angela K. Wilson:
Molecular Screening and Toxicity Estimation of 260, 000 Perfluoroalkyl and Polyfluoroalkyl Substances (PFASs) through Machine Learning. 4569-4578 - Zhipeng Wu, Xiang Cai, Chengyun Zhang, Haoran Qiao, Yejian Wu, Yun Zhang, Xinqiao Wang, Haiying Xie, Feng Luo, Hongliang Duan:
Self-Supervised Molecular Pretraining Strategy for Low-Resource Reaction Prediction Scenarios. 4579-4590 - Simon Bray, Victor Tänzel, Steffen Wolf:
Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods. 4591-4604 - Billy J. Williams-Noonan, Melissa N. Speer, Tu C. Le, Maiada M. Sadek, Philip E. Thompson, Raymond S. Norton, Elizabeth Yuriev, Nicholas Barlow, David K. Chalmers, Irene Yarovsky:
Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. 4605-4619 - María Isabel Sánchez-Rodríguez, Elena Sánchez-López, Alberto Marinas, José María Caridad, Francisco José Urbano:
Redundancy Analysis to Reduce the High-Dimensional Near-Infrared Spectral Information to Improve the Authentication of Olive Oil. 4620-4628 - Yuchi Qiu, Guo-Wei Wei:
CLADE 2.0: Evolution-Driven Cluster Learning-Assisted Directed Evolution. 4629-4641 - Agamemnon Krasoulis, Nick Antonopoulos, Vassilis Pitsikalis, Stavros Theodorakis:
DENVIS: Scalable and High-Throughput Virtual Screening Using Graph Neural Networks with Atomic and Surface Protein Pocket Features. 4642-4659 - Matteo Aldeghi, David E. Graff, Nathan C. Frey, Joseph A. Morrone, Edward O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley:
Roughness of Molecular Property Landscapes and Its Impact on Modellability. 4660-4671 - Bo Yang, David Hawley, Jianhua Yao, Camille May, Jose E. Mendez-Arroyo, Daniel H. Ess:
Demonstration of High-Throughput Building Block and Composition Analysis of Metal-Organic Frameworks. 4672-4679 - Uschi Dolfus, Hans Briem, Matthias Rarey:
Visualizing Generic Reaction Patterns. 4680-4689 - Denys E. S. Santos, Kaline Coutinho, Thereza A. Soares:
Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. 4690-4701 - Alex S. Moraes, Gabriel A. Pinheiro, Tuanan C. Lourenço, Mauro C. Lopes, Marcos G. Quiles, Luis Gustavo Dias, Juarez L. F. Da Silva:
Screening of the Role of the Chemical Structure in the Electrochemical Stability Window of Ionic Liquids: DFT Calculations Combined with Data Mining. 4702-4712 - Julián A. Delgado, Vered Wineman-Fisher, Sagar Pandit, Sameer Varma:
Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions. 4713-4726 - Surajit Nandi, Jonas Busk, Peter Bjørn Jørgensen, Tejs Vegge, Arghya Bhowmik:
Cheap Turns Superior: A Linear Regression-Based Correction Method to Reaction Energy from the DFT. 4727-4735 - Tianyi Ding, Dmitry Karlov, Almudena Pino-Ángeles, Irina G. Tikhonova:
Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. 4736-4747 - Bruno Giovanni Galuzzi, Antonio Mirarchi, Edoardo Luca Viganò, Luca De Gioia, Chiara Damiani, Federica Arrigoni:
Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. 4748-4759 - Melisa E. Gantner, Denis N. Prada Gori, Manuel A. Llanos, Alan Talevi, Andrea Angeli, Daniela Vullo, Claudiu T. Supuran, Luciana Gavernet:
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening. 4760-4770 - Anastasia Croitoru, Alexey Aleksandrov:
Parametrization of Force Field Bonded Terms under Structural Inconsistency. 4771-4782 - Jirí Vymetal, Jirí Vondrásek:
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. 4783-4798 - Alan Fernando Rodríguez Serrano, I-Ming Hsing:
Prediction of Aptamer-Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations. 4799-4809 - Santhosh Sankar, Naren Chandran Sakthivel, Nagasuma Chandra:
Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment. 4810-4819 - Quang-Hien Kha, Quang-Thai Ho, Nguyen-Quoc-Khanh Le:
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles. 4820-4826
Volume 62, Number 20, October 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Saba Iftkhar, Alex G. C. de Sá, João P. L. Velloso, Raghad Al-Jarf, Douglas E. V. Pires, David B. Ascher:
cardioToxCSM: A Web Server for Predicting Cardiotoxicity of Small Molecules. 4827-4836 - Megumi Iwayama, Stephen Wu, Chang Liu, Ryo Yoshida:
Functional Output Regression for Machine Learning in Materials Science. 4837-4851 - Hisham Abdel-Aty, Ian R. Gould:
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting. 4852-4862 - Sara Romeo Atance, Juan Viguera Diez, Ola Engkvist, Simon Olsson, Rocío Mercado:
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models. 4863-4872 - Chuan Li, Chenghui Wang, Ming Sun, Yan Zeng, Yuan Yuan, Qiaolin Gou, Guangchuan Wang, Yanzhi Guo, Xuemei Pu:
Correlated RNN Framework to Quickly Generate Molecules with Desired Properties for Energetic Materials in the Low Data Regime. 4873-4887 - Gabriel Sinclair, Inthirany Thillainadarajah, Brian Meyer, Vicente Samano, Sakuntala Sivasupramaniam, Linda Adams, Egon L. Willighagen, Ann M. Richard, Martin Walker, Antony J. Williams:
Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. 4888-4905 - Matthew S. Johnson, Xiaorui Dong, Alon Grinberg Dana, Yunsie Chung, David Farina, Ryan J. Gillis, Mengjie Liu, Nathan W. Yee, Katrin Blondal, Emily J. Mazeau, Colin A. Grambow, A. Mark Payne, Kevin A. Spiekermann, Hao-Wei Pang, C. Franklin Goldsmith, Richard H. West, William H. Green Jr.:
RMG Database for Chemical Property Prediction. 4906-4915 - Angela Parise, Giada Ciardullo, Mario Prejanò, Aurélien de la Lande, Tiziana Marino:
On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. 4916-4927 - Qingqing Jia, Yifan Ni, Ziteng Liu, Xu Gu, Ziyi Cui, Mengting Fan, Qiang Zhu, Yi Wang, Jing Ma:
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests. 4928-4936 - Amanda E. Wakefield, Dávid Bajusz, Dima Kozakov, György M. Keserü, Sandor Vajda:
Conservation of Allosteric Ligand Binding Sites in G-Protein Coupled Receptors. 4937-4954 - Rudramani Pokhrel, Rojesh Shakya, Prabin Baral, Prem Chapagain:
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. 4955-4962 - Lukács J. Németh, Tamás A. Martinek, Balázs Jójárt:
Tilted State Population of Antimicrobial Peptide PGLa Is Coupled to the Transmembrane Potential. 4963-4969 - Xiaochen Cui, Hao Liu, Hai-Feng Chen:
Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization. 4970-4982 - Haiyi Zhang, Xiyao Zhang, Guanhong Huang, Feifei Li, Fengmei Wu, Chunfang Xie, Daling Liu, Dongsheng Yao:
Screening ssDNA Aptamers Against Human Vascular Endothelial Factor 165 via Semirational Design. 4983-4991 - Isabell Louise Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi:
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. 4992-5008 - Xin Yang, Guifeng Lin, Anjie Xia, Jingming Liu, Shiyu Zhang, Pei Zhou, Yiwei Wang, Jiahao Zhang, Yangli Zhou, Pei Chen, Yifei Wang, Tao Zheng, Linli Li, Sheng-Yong Yang:
Discovery of Small Molecule Agonist of Gonadotropin-Releasing Hormone Receptor (GnRH1R). 5009-5022 - Carla F. Sousa, Mohamed A. M. Kamal, Robert Richter, Kalanika Elamaldeniya, Rolf W. Hartmann, Martin Empting, Claus-Michael Lehr, Olga V. Kalinina:
Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. 5023-5033
Volume 62, Number 21, November 2022
- Guo-Wei Wei, Thereza A. Soares, Habibah A. Wahab, Feng Zhu:
Computational Chemistry in Asia. 5035-5037 - Pengcheng Xu, Dongping Chang, Tian Lu, Long Li, Minjie Li, Wencong Lu:
Search for ABO3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies. 5038-5049 - Thanh-Hoang Nguyen-Vo, Quang H. Trinh, Loc Nguyen, Trang T. T. Do, Matthew Chin Heng Chua, Binh P. Nguyen:
Predicting Antimalarial Activity in Natural Products Using Pretrained Bidirectional Encoder Representations from Transformers. 5050-5058 - Thanh-Hoang Nguyen-Vo, Quang H. Trinh, Loc Nguyen, Phuong-Uyen Nguyen-Hoang, Thien-Ngan Nguyen, Dung T. Nguyen, Binh P. Nguyen, Ly Le:
iCYP-MFE: Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding. 5059-5068 - Rishal Aggarwal, Akash Gupta, Vineeth R. Chelur, C. V. Jawahar, U. Deva Priyakumar:
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks. 5069-5079 - Loc Nguyen, Thanh-Hoang Nguyen-Vo, Quang H. Trinh, Bach Hoai Nguyen, Phuong-Uyen Nguyen-Hoang, Ly Le, Binh P. Nguyen:
iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation. 5080-5089 - Wenze Li, Donghan Wang, Zirui Yang, Huijie Zhang, Li Hong Hu, Guanhua Chen:
DeepNCI: DFT Noncovalent Interaction Correction with Transferable Multimodal Three-Dimensional Convolutional Neural Networks. 5090-5099 - Sowmya Ramaswamy Krishnan, Navneet Bung, Sarveswara Rao Vangala, Rajgopal Srinivasan, Gopalakrishnan Bulusu, Arijit Roy:
De Novo Structure-Based Drug Design Using Deep Learning. 5100-5109 - Mengrong Li, Miaomiao Li, Jingjing Guo:
Molecular Mechanism of Ca2+ in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. 5110-5119 - Fuhui Zhang, Xin Chen, Jianfang Chen, Yanjiani Xu, Shiqi Li, Yanzhi Guo, Xuemei Pu:
Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation. 5120-5135 - Yang Wang:
Extension and Quantification of the Fries Rule and Its Connection to Aromaticity: Large-Scale Validation by Wave-Function-Based Resonance Analysis. 5136-5148 - Donghui Huo, Shiyu Wang, Yue Kong, Zijian Qin, Aixia Yan:
Discovery of Novel Epidermal Growth Factor Receptor (EGFR) Inhibitors Using Computational Approaches. 5149-5164 - Shaoli Cui, Weijia Zhang, Xueguang Shao, Wensheng Cai:
Hyperactive Antifreeze Proteins Promote Ice Growth before Binding to It. 5165-5174 - Jianfang Chen, Jiangting Liu, Yuan Yuan, Xin Chen, Fuhui Zhang, Xuemei Pu:
Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor. 5175-5192 - Rabindranath Paul, Siddhartha Bera, Madhusmita Devi, Sandip Paul:
Inhibition of Aβ16-22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study. 5193-5207 - Guoqin Feng, Xiangying Zhang, Yan Li, Renxiao Wang:
Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations. 5208-5222 - Yunyuan Huang, Jiqun Wang, Jiaqi Liu, Donglei Shi, Xiaokang Li, Manjiong Wang, Taotao Lu, Bei Jiang, Conglong Xia, Houwen Lin, Yixiang Xu, Jian Li:
Rapid Repurposing of Novel Combination Drugs for the Treatment of Heart Failure via a Computationally Guided Network Screening Approach. 5223-5232 - Haiyi Chen, Rui Zhou, Jinping Pang, Yue Guo, Jiawen Chen, Yu Kang, Mojie Duan, Tingjun Hou:
Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands. 5233-5245 - Dongxiao Hao, He Wang, Yongjian Zang, Lei Zhang, Zhiwei Yang, Shengli Zhang:
Mechanism of Glycans Modulating Cholesteryl Ester Transfer Protein: Unveiled by Molecular Dynamics Simulation. 5246-5257 - Yibo Wang, Siru Wu, Cong Zhang, Yushan Jin, Xiaohui Wang:
Dissecting the Role of N-Glycan at N413 in Toll-like Receptor 3 via Molecular Dynamics Simulations. 5258-5266 - Wanqian Dong, Rui Zhou, Jiawen Chen, Zhengyu Shu, Mojie Duan:
Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein. 5267-5275 - Maywan Hariono, Dominikus B. E. Wijaya, Teddy Chandra, Nico Frederick, Agnes B. Putri, Erlia Herawati, Luthfi A. Warastika, Merry Permatasari, Agata D. A. Putri, Satrio Ardyantoro:
A Decade of Indonesian Atmosphere in Computer-Aided Drug Design. 5276-5288 - Yunshuo Zhao, Xiaotong Chen, Zhe Ding, Chuanjie He, Guanfei Gao, Sifan Lyu, Yanfeng Gao, Jiangfeng Du:
Identification of Novel CD39 Inhibitors Based on Virtual Screening and Enzymatic Assays. 5289-5304 - Richa Mardianingrum, Maywan Hariono, Ruswanto Ruswanto, Muhammad Yusuf, Muchtaridi Muchtaridi:
Synthesis, Anticancer Activity, Structure-Activity Relationship, and Molecular Modeling Studies of α-Mangostin Derivatives as hERα Inhibitor. 5305-5316
Volume 62, Number 22, November 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Thereza A. Soares, Ariane Nunes-Alves, Angelica Mazzolari, Fiorella Ruggiu, Guo-Wei Wei, Kenneth M. Merz Jr.:
The (Re)-Evolution of Quantitative Structure-Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. 5317-5320 - Youjun Xu, Jinchuan Xiao, Chia-Han Chou, Jianhang Zhang, Jintao Zhu, Qiwan Hu, Hemin Li, Ningsheng Han, Bingyu Liu, Shuaipeng Zhang, Jinyu Han, Zhen Zhang, Shuhao Zhang, Weilin Zhang, Luhua Lai, Jianfeng Pei:
MolMiner: You Only Look Once for Chemical Structure Recognition. 5321-5328 - Fergus Boyles, Charlotte M. Deane, Garrett M. Morris:
Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained on Docked Poses. 5329-5341 - Connor J. Morris, Jacob A. Stern, Brenden Stark, Max Christopherson, Dennis Della Corte:
MILCDock: Machine Learning Enhanced Consensus Docking for Virtual Screening in Drug Discovery. 5342-5350 - Tatsuya Yoshizawa, Shoichi Ishida, Tomohiro Sato, Masateru Ohta, Teruki Honma, Kei Terayama:
Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search. 5351-5360 - Zewei Ji, Runhan Shi, Jiarui Lu, Fang Li, Yang Yang:
ReLMole: Molecular Representation Learning Based on Two-Level Graph Similarities. 5361-5372 - Zhen Liu, Tetiana Zubatiuk, Adrian E. Roitberg, Olexandr Isayev:
Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials. 5373-5382 - Oliver B. Scott, Jing Gu, A. W. Edith Chan:
Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network. 5383-5396 - Joshua L. Lansford, Brian C. Barnes, Betsy M. Rice, Klavs F. Jensen:
Building Chemical Property Models for Energetic Materials from Small Datasets Using a Transfer Learning Approach. 5397-5410 - Rodrigo S. Hormazabal, Jeong Won Kang, Kiho Park, Dae Ryook Yang:
Not from Scratch: Predicting Thermophysical Properties through Model-Based Transfer Learning Using Graph Convolutional Networks. 5411-5424 - Alberto Celma, Richard Bade, Juan Vicente Sancho, Félix Hernandez, Melissa Humphries, Lubertus Bijlsma:
Prediction of Retention Time and Collision Cross Section (CCSH+, CCSH-, and CCSNa+) of Emerging Contaminants Using Multiple Adaptive Regression Splines. 5425-5434 - Evan R. Antoniuk, Peggy Li, Bhavya Kailkhura, Anna M. Hiszpanski:
Representing Polymers as Periodic Graphs with Learned Descriptors for Accurate Polymer Property Predictions. 5435-5445 - Pin Chen, Rui Jiao, Jinyu Liu, Yang Liu, Yutong Lu:
Interpretable Graph Transformer Network for Predicting Adsorption Isotherms of Metal-Organic Frameworks. 5446-5456 - Kaycee Low, Michelle L. Coote, Ekaterina I. Izgorodina:
Explainable Solvation Free Energy Prediction Combining Graph Neural Networks with Chemical Intuition. 5457-5470 - William Bort, Daniyar Mazitov, Dragos Horvath, Fanny Bonachéra, Arkadii I. Lin, Gilles Marcou, Igor I. Baskin, Timur I. Madzhidov, Alexandre Varnek:
Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder. 5471-5484 - Hui Zhu, Jincai Yang, Niu Huang:
Assessment of the Generalization Abilities of Machine-Learning Scoring Functions for Structure-Based Virtual Screening. 5485-5502 - João Paulo Almeida de Mendonça, Felipe V. Calderan, Tuanan C. Lourenço, Marcos G. Quiles, Juarez L. F. Da Silva:
Theoretical Framework Based on Molecular Dynamics and Data Mining Analyses for the Study of Potential Energy Surfaces of Finite-Size Particles. 5503-5512 - Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Representing Catalytic Mechanisms with Rule Composition. 5513-5524 - Bas van Beek, Juliette Zito, Lucas Visscher, Ivan Infante:
CAT: A Compound Attachment Tool for the Construction of Composite Chemical Compounds. 5525-5535 - Sonia Ziada, Julien Diharce, Eric Raimbaud, Samia Aci-Sèche, Pierre Ducrot, Pascal Bonnet:
Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations. 5536-5549 - Yanjun Li, Daohong Zhou, Guangrong Zheng, Xiaolin Li, Dapeng Wu, Yaxia Yuan:
DyScore: A Boosting Scoring Method with Dynamic Properties for Identifying True Binders and Nonbinders in Structure-Based Drug Discovery. 5550-5567 - Iñigo Iribarren, Cristina Trujillo:
Efficiency and Suitability when Exploring the Conformational Space of Phase-Transfer Catalysts. 5568-5580 - Xin Chen, Yuan Yuan, Yichi Chen, Jin Yu, Jingzhou Wang, Jianfang Chen, Yanzhi Guo, Xuemei Pu:
Biased Activation Mechanism Induced by GPCR Heterodimerization: Observations from μOR/δOR Dimers. 5581-5600 - Robert J. Cordina, Beccy Smith, Tell Tuttle:
Rapid Automated Quantification of Triacylglyceride Crystallinity in Molecular Dynamics Simulations. 5601-5606 - Soumyo Sen, Aleksandar Spasic, Anjana Sinha, Jialing Wang, Martin Bush, Jihong Li, Dragana Nesic, Yuchen Zhou, Gabriella Angiulli, Paul Morgan, Leslie Salas-Estrada, Junichi Takagi, Thomas Walz, Barry S. Coller, Marta Filizola:
Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. 5607-5621 - Joshua T. Horton, Simon Boothroyd, Jeffrey Wagner, Joshua A. Mitchell, Trevor Gokey, David L. Dotson, Pavan Kumar Behara, Venkata Krishnan Ramaswamy, Mark Mackey, John D. Chodera, Jamshed Anwar, David L. Mobley, Daniel J. Cole:
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. 5622-5633 - Tom Frömbgen, Jan Blasius, Vahideh Alizadeh, Alain Chaumont, Martin Brehm, Barbara Kirchner:
Cluster Analysis in Liquids: A Novel Tool in TRAVIS. 5634-5644 - Wenlang Liu, Zhenhao Liu, Hao Liu, Lance M. Westerhoff, Zheng Zheng:
Free Energy Calculations Using the Movable Type Method with Molecular Dynamics Driven Protein-Ligand Sampling. 5645-5665 - Austin M. Cool, Steffen Lindert:
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. 5666-5674 - Eric R. Hantz, Steffen Lindert:
Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors. 5675-5687 - Yanru Ji, Ying Fang, Jianhua Wu:
Tension Enhances the Binding Affinity of β1 Integrin by Clamping Talin Tightly: An Insight from Steered Molecular Dynamics Simulations. 5688-5698 - Keigo Gohda:
Conformational Analysis of the Loop-to-Helix Transition of the α-Helix3 Plastic Region in the N-Terminal Domain of Human Hsp90α by a Computational Biochemistry Approach. 5699-5714 - Matteo Pavan, Silvia Menin, Davide Bassani, Mattia Sturlese, Stefano Moro:
Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations. 5715-5728 - Jiao Zhou, Wei Li, Shanyue Guan, Xiaohong Chen, Xiang Liu, Weiyan Shao:
Discovery of Chemokine CXCL12 Inhibitors by Tandem Application of Virtual Screening and NMR Spectrometry. 5729-5737 - Xavier Daura, Oscar Conchillo-Solé:
On Quality Thresholds for the Clustering of Molecular Structures. 5738-5745 - Vinicius Gonçalves Maltarollo, Ekaterina Shevchenko, Igor Daniel de Miranda Lima, Elio A. Cino, Glaucio Monteiro Ferreira, Antti Poso, Thales Kronenberger:
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels. 5746-5761 - Tingting Fu, Hongxing Zhang, Qingchuan Zheng:
Molecular Insights into the Heterotropic Allosteric Mechanism in Cytochrome P450 3A4-Mediated Midazolam Metabolism. 5762-5770 - Nil Casajuana-Martin, Gemma Navarro, Angel Gonzalez, Claudia Llinas del Torrent, Marc Gómez-Autet, Aleix Quintana García, Rafael Franco, Leonardo Pardo:
A Single Point Mutation Blocks the Entrance of Ligands to the Cannabinoid CB2 Receptor via the Lipid Bilayer. 5771-5779 - Ying Wang, Huan Wang, Yupeng Zhang, Feng Xu, Jian Wang, Fengjiao Zhang:
Stepwise Strategy to Identify Thrombin as a Hydrolytic Substrate for Nattokinase. 5780-5793 - Francesca Picarazzi, Marika Zuanon, Gaia Pasqualetto, Silvia Cammarone, Isabella Romeo, Mark T. Young, Andrea Brancale, Marcella Bassetto, Mattia Mori:
Identification of Small Molecular Chaperones Binding P23H Mutant Opsin through an In Silico Structure-Based Approach. 5794-5805 - Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu, Sheng-You Huang:
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. 5806-5820 - Janez Konc, Dusanka Janezic:
ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites. 5821-5829 - Ruihan Dong, Hongpeng Yang, Chengwei Ai, Guihua Duan, Jianxin Wang, Fei Guo:
DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction. 5830-5840 - Bailu Yan, Xinchun Ran, Anvita Gollu, Zihao Cheng, Xiang Zhou, Yiwen Chen, Zhongyue J. Yang:
IntEnzyDB: an Integrated Structure-Kinetics Enzymology Database. 5841-5848
Volume 62, Number 23, December 2022
- Martin J. Field:
pDynamo3 Molecular Modeling and Simulation Program. 5849-5854 - Georgios Iakovou, Stephen D. Laycock, Steven Hayward:
Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT. 5855-5861 - Xiujuan Ou, Yi Zhang, Yiduo Xiong, Yi Xiao:
Advances in RNA 3D Structure Prediction. 5862-5874 - Minjie Mou, Ziqi Pan, Mingkun Lu, Huaicheng Sun, Yunxia Wang, Yongchao Luo, Feng Zhu:
Application of Machine Learning in Spatial Proteomics. 5875-5895 - Eugene Raush, Ruben Abagyan, Maxim Totrov:
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. 5896-5906 - Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang:
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. 5907-5917 - Ravithree D. Senanayake, Xiaoxiao Yao, Clarice E. Froehlich, Meghan S. Cahill, Trever R. Sheldon, Mary McIntire, Christy L. Haynes, Rigoberto Hernandez:
Machine Learning-Assisted Carbon Dot Synthesis: Prediction of Emission Color and Wavelength. 5918-5928 - Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu, Jiaxuan Zhang:
Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. 5929-5937 - Derek van Tilborg, Alisa Alenicheva, Francesca Grisoni:
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs. 5938-5951 - Youngchun Kwon, Sun Kim, Youn-Suk Choi, Seokho Kang:
Generative Modeling to Predict Multiple Suitable Conditions for Chemical Reactions. 5952-5960 - Shuang Wang, Wenqi Chen, Peifu Han, Xue Li, Tao Song:
RGN: Residue-Based Graph Attention and Convolutional Network for Protein-Protein Interaction Site Prediction. 5961-5974 - Jialu Wu, Junmei Wang, Zhenxing Wu, Shengyu Zhang, Yafeng Deng, Yu Kang, Dong-Sheng Cao, Chang-Yu Hsieh, Tingjun Hou:
ALipSol: An Attention-Driven Mixture-of-Experts Model for Lipophilicity and Solubility Prediction. 5975-5987 - Satoshi Noguchi, Junya Inoue:
Exploration of Chemical Space Guided by PixelCNN for Fragment-Based De Novo Drug Discovery. 5988-6001 - Maximilian Beckers, Nikolas Fechner, Nikolaus Stiefl:
25 Years of Small-Molecule Optimization at Novartis: A Retrospective Analysis of Chemical Series Evolution. 6002-6021 - Xiaowen Dai, Yuan Xu, Haodi Qiu, Xu Qian, Mingde Lin, Lin Luo, Yang Zhao, Dingfang Huang, Yanmin Zhang, Yadong Chen, Haichun Liu, Yulei Jiang:
KID: A Kinase-Focused Interaction Database and Its Application in the Construction of Kinase-Focused Molecule Databases. 6022-6034 - Xia Zhao, Yuhao Sun, Ruiqiu Zhang, Zhaoyang Chen, Yuqing Hua, Pei Zhang, Huizhu Guo, Xueyan Cui, Xin Huang, Xiao Li:
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity. 6035-6045 - Fan Hu, Dongqi Wang, Huazhen Huang, Yishen Hu, Peng Yin:
Bridging the Gap between Target-Based and Cell-Based Drug Discovery with a Graph Generative Multitask Model. 6046-6056 - Xiao-Kang Guo, Yingkai Zhang:
CovBinderInPDB: A Structure-Based Covalent Binder Database. 6057-6068 - Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Tai-Sung Lee, Timothy J. Giese, Darrin M. York:
AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA). 6069-6083 - Han Zhang, Seonghoon Kim, Wonpil Im:
Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations. 6084-6093 - Lorenzo D'amore, David F. Hahn, David L. Dotson, Joshua T. Horton, Jamshed Anwar, Ian Craig, Thomas Fox, Alberto Gobbi, Sirish Kaushik Lakkaraju, Xavier Lucas, Katharina Meier, David L. Mobley, Arjun Narayanan, Christina E. M. Schindler, William C. Swope, Pieter J. in 't Veld, Jeffrey Wagner, Bai Xue, Gary Tresadern:
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. 6094-6104 - Jelena Tosovic, Domagoj Fijan, Marko Jukic, Urban Bren:
Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data. 6105-6117 - Jianzhong Chen, Qingkai Zeng, Wei Wang, Haibo Sun, Guodong Hu:
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations. 6118-6132 - Perumal Manivel, Parthiban Marimuthu, Sun Yu, Xiumin Chen:
Multispectroscopic and Computational Investigations on the Binding Mechanism of Dicaffeoylquinic Acids with Ovalbumin. 6133-6147 - Tianyi Yang, Li Han, Shuanghong Huo:
Dynamics and Allosteric Information Pathways of Unphosphorylated c-Cbl. 6148-6159 - Lin Wang, Fenglei Li, Xin-yue Ma, Yong Cang, Fang Bai:
PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method. 6160-6171 - Yang Zhou, Junhao Li, Glib Baryshnikov, Yaoquan Tu:
Unraveling the Abnormal Molecular Mechanism of Suicide Inhibition of Cytochrome P450 3A4. 6172-6181 - Klaudia Mráziková, Holger Kruse, Vojtech Mlýnský, Pascal Auffinger, Jirí Sponer:
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. 6182-6200 - Eric R. Hantz, Steffen Lindert:
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. 6201-6208 - Dominykas Lukauskis, Marley L. Samways, Simone Aureli, Benjamin P. Cossins, Richard D. Taylor, Francesco Luigi Gervasio:
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses. 6209-6216 - Takunori Yasuda, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada:
Protein Structure Validation Derives a Smart Conformational Search in a Physically Relevant Configurational Subspace. 6217-6227 - James Vergilio, Christopher Lockhart, Dmitri K. Klimov:
De Novo Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer. 6228-6241 - Andreas Denger, Volkhard Helms:
Optimized Data Set and Feature Construction for Substrate Prediction of Membrane Transporters. 6242-6257 - Deng Pan, Lijun Quan, Zhi Jin, Taoning Chen, Xuejiao Wang, Jingxin Xie, Tingfang Wu, Qiang Lyu:
Multisource Attention-Mechanism-Based Encoder-Decoder Model for Predicting Drug-Drug Interaction Events. 6258-6270 - Zhenqiu Shu, Qinghan Long, Luping Zhang, Zhengtao Yu, Xiao-Jun Wu:
Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering. 6271-6286
Volume 62, Number 24, December 2022
- Issue Publication Information.
- Issue Editorial Masthead.
- Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro:
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. 6287-6291 - Chrystal D. Bruce, Patricia M. Flatt, Sarah R. Kirk, Elizabeth Roberts-Kirchhoff, Hala G. Schepmann:
The Value of Peer Mentoring Networks for Developing Leaders and Inspiring Change. 6292-6296 - Michele Cascella, Thereza A. Soares:
Bias Amplification in Gender, Gender Identity, and Geographical Affiliation. 6297-6301 - Yuxiang Wang, Alper Kiziltas, Patrick Blanchard, Tiffany R. Walsh:
ContactAngleCalculator: An Automated, Parametrized, and Flexible Code for Contact Angle Estimation in Visual Molecular Dynamics. 6302-6308 - Deborah Palazzotti, Martina Fiorelli, Stefano Sabatini, Serena Massari, Maria Letizia Barreca, Andrea Astolfi:
Q-raKtion: A Semiautomated KNIME Workflow for Bioactivity Data Points Curation. 6309-6315 - Kelly Anderson, Sarah Arradondo, K. Aurelia Ball, Chrystal D. Bruce, Maria A. Gomez, Kedan He, Heidi Hendrickson, Lindsey Madison, Ashley Ringer McDonald, Maria C. Nagan, Caitlin E. Scott, Patricia Soto, Aimée Tomlinson, Mychel Varner, Carol A. Parish:
The Impacts of the Molecular Education and Research Consortium in Undergraduate Computational Chemistry on the Careers of Women in Computational Chemistry. 6316-6322 - Alzbeta Türková, Brandon J. Bongers, Ulf Norinder, Orsolya Ungvári, Virág Székely, Andrey Tarnovskiy, Gergely Szakács, Csilla Özvegy-Laczka, Gerard J. P. van Westen, Barbara Zdrazil:
Identifying Novel Inhibitors for Hepatic Organic Anion Transporting Polypeptides by Machine Learning-Based Virtual Screening. 6323-6335 - Megan A. Lim, Song Yang, Huanghao Mai, Alan C. Cheng:
Exploring Deep Learning of Quantum Chemical Properties for Absorption, Distribution, Metabolism, and Excretion Predictions. 6336-6341 - María Jimena Martínez, María Virginia Sabando, Axel J. Soto, Carlos Roca, Carlos Requena-Triguero, Nuria E. Campillo, Juan A. Páez, Ignacio Ponzoni:
Multitask Deep Neural Networks for Ames Mutagenicity Prediction. 6342-6351 - Rangsiman Ketkaew, Sandra Luber:
DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space. 6352-6364 - Shu Huang, Jacqueline M. Cole:
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement. 6365-6377 - Swati Baskiyar, Chang Ren, Kabre L. Heck, Audrey M. Hall, Muhammad Gulfam, Sadaira Packer, Cheryl D. Seals, Angela I. Calderón:
Bioactive Natural Products Identification Using Automation of Molecular Networking Software. 6378-6385 - Neetu Tripathi, Manoj Kumar Goshisht:
Advancing Women in Chemistry: A Step Toward Gender Parity. 6386-6397 - Marko Babic, Patrizia Jankovic, Silvia Marchesan, Goran Mausa, Daniela Kalafatovic:
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. 6398-6410 - Soma Roy, Santanu Bhattacharya:
Chemical Information and Computational Modeling of Targeting Hybrid Nucleic Acid Structures of PIM1 Sequences by Synthetic Pyrrole-Imidazole Carboxamide Drugs. 6411-6422 - Juan Antonio Seijas-Bellido, Bipasa Samanta, Karen Valadez-Villalobos, Juan Jesús Gallardo, Javier Navas, Salvador R. G. Balestra, Rafael María Madero Castro, José Manuel Vicent-Luna, Shuxia Tao, Maytal Caspary Toroker, Juan Antonio Anta:
Transferable Classical Force Field for Pure and Mixed Metal Halide Perovskites Parameterized from First-Principles. 6423-6435 - Christina Eleftheria Tzeliou, Demeter Tzeli:
3-Input AND Molecular Logic Gate with Enhanced Fluorescence Output: The Key Atom for the Accurate Prediction of the Spectra. 6436-6448 - Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane, Rajendra Joshi:
Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain. 6449-6461 - Milla Kurki, Antti Poso, Piia Bartos, Markus S. Miettinen:
Structure of POPC Lipid Bilayers in OPLS3e Force Field. 6462-6474 - Jay-Anne K. Johnson, Isaiah Sumner:
On the Possibility That Bond Strain Is the Mechanism of RING E3 Activation in the E2-Catalyzed Ubiquitination Reaction. 6475-6481 - Ke Wang, Xueguang Shao, Wensheng Cai:
Binding Models of Aβ42 Peptide with Membranes Explored by Molecular Simulations. 6482-6493 - María Lucrecia Bogado, Roxana Noelia Villafañe, José Leonardo Gómez Chavez, Emilio Luis Angelina, Gladis Laura Sosa, Nélida María Peruchena:
Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen Environment. 6494-6507 - Paptawan Thongdee, Chayanin Hanwarinroj, Bongkochawan Pakamwong, Pharit Kamsri, Auradee Punkvang, Jiraporn Leanpolchareanchai, Sombat Ketrat, Patchreenart Saparpakorn, Supa Hannongbua, Kanchiyaphat Ariyachaokun, Khomson Suttisintong, Sanya Sureram, Prasat Kittakoop, Poonpilas Hongmanee, Pitak Santanirand, Galina V. Mukamolova, Rosemary A. Blood, Yuiko Takebayashi, James Spencer, Adrian J. Mulholland, Pornpan Pungpo:
Virtual Screening Identifies Novel and Potent Inhibitors of Mycobacterium tuberculosis PknB with Antibacterial Activity. 6508-6518 - Alexandra V. Krivitskaya, Maria G. Khrenova:
Interplay between the Enamine and Imine Forms of the Hydrolyzed Imipenem in the Active Sites of Metallo-β-lactamases and in Water Solution. 6519-6529 - Alexsander C. Vendite, Thereza A. Soares, Kaline Coutinho:
The Effect of Surface Composition on the Selective Capture of Atmospheric CO2 by ZIF Nanoparticles: The Case of ZIF-8. 6530-6543 - Akie Kowaguchi, Katsuhiro Endo, Paul E. Brumby, Kentaro Nomura, Kenji Yasuoka:
Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies. 6544-6552 - Lucianna Helene Santos, Thales Kronenberger, Renata G. Almeida, Elany B. Silva, Rafael E. O. Rocha, Joyce C. Oliveira, Luiza V. Barreto, Danielle Skinner, Pavla Fajtová, Miriam A. Giardini, Brendon Woodworth, Conner Bardine, André L. Lourenço, Charles S. Craik, Antti Poso, Larissa M. Podust, James H. McKerrow, Jair L. Siqueira-Neto, Anthony J. O'Donoghue, Eufrânio N. da Silva Júnior, Rafaela Salgado Ferreira:
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2. 6553-6573 - Gaurav Sharma, Lin Frank Song, Kenneth M. Merz Jr.:
Effect of an Inhibitor on the ACE2-Receptor-Binding Domain of SARS-CoV-2. 6574-6585 - Marius T. Wenz, Miriam Bertazzon, Jana Sticht, Stevan Aleksic, Daniela Gjorgjevikj, Christian Freund, Bettina G. Keller:
Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW. 6586-6601 - Emmanuel E. Moutoussamy, Hanif M. Khan, Mary F. Roberts, Anne Gershenson, Christophe Chipot, Nathalie Reuter:
Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C. 6602-6613 - Agustín Ormazábal, Gustavo Pierdominici-Sottile, Juliana Palma:
Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations. 6614-6627 - Sree Kavya Penneru, Moumita Saharay, Marimuthu Krishnan:
CelS-Catalyzed Processive Cellulose Degradation and Cellobiose Extraction for the Production of Bioethanol. 6628-6638 - Yongjian Zang, He Wang, Dongxiao Hao, Ying Kang, Jianwen Zhang, Xuhua Li, Lei Zhang, Zhiwei Yang, Shengli Zhang:
p38α Kinase Auto-Activation through Its Conformational Transition Induced by Tyr323 Phosphorylation. 6639-6648 - Krystel El Hage, Giovanni Ribaudo, Louis Lagardère, Alberto Ongaro, Philippe H. Kahn, Luc Demange, Jean-Philip Piquemal, Giuseppe Zagotto, Nohad Gresh:
Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. 6649-6666 - Shuangyan Zhou, Huizhen Zou, Yu Wang, Glenn V. Lo, Shuai Yuan:
Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations. 6667-6678 - Shalini Yadav, Vandana Kardam, Ankita Tripathi, Shruti T. G, Kshatresh Dutta Dubey:
The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes. 6679-6690 - Riccardo Rozza, Andrea Saltalamacchia, Clarissa Orrico, Pavel Janos, Alessandra Magistrato:
All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition. 6691-6703 - Jozica Dolenc, Esme J. Haywood, Tingting Zhu, Lorna J. Smith:
Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds. 6704-6714 - Ebru Çetin, Ali Rana Atilgan, Canan Atilgan:
DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. 6715-6726 - Lei Chen, Weikang Gong, Zhongjie Han, Wenxue Zhou, Shuang Yang, Chunhua Li:
Key Residues in δ Opioid Receptor Allostery Explored by the Elastic Network Model and the Complex Network Model Combined with the Perturbation Method. 6727-6738 - Alessio Bartocci, Gilberto Pereira, Marco Cecchini, Elise Dumont:
Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. 6739-6748 - Sharon Emily Stone, Dhiman Ray, Ioan Andricioaei:
Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. 6749-6761 - Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino:
Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. 6762-6774 - Volkan Findik, Betül Tuba Varinca Gerçik, Öykü Sinek, Safiye Sag Erdem, Manuel F. Ruiz-López:
Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM: QM Computations. 6775-6787 - Lisbeth Ravnkilde Kjølbye, Lars Sørensen, Jun Yan, Nils A. Berglund, Jesper Ferkinghoff-Borg, Carol V. Robinson, Birgit Schiøtt:
Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P2 Lipids. 6788-6802 - Karolina Mitusinska, Maria Bzówka, Tomasz Magdziarz, Artur Góra:
Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls. 6803-6811 - Daniela Trisciuzzi, Lydia Siragusa, Massimo Baroni, Gabriele Cruciani, Orazio Nicolotti:
An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening. 6812-6824 - Melina Mottin, Bruna Katiele de Paula Sousa, Nathalya Cristina de Moraes Roso Mesquita, Ketllyn Irene Zagato de Oliveira, Gabriela Dias Noske, Geraldo Rodrigues Sartori, Aline Albuquerque, Fabio Urbina, Ana C. Puhl, José Teófilo Moreira-Filho, Guilherme E. Souza, Rafael V. C. Guido, Eugene N. Muratov, Bruno Junior Neves, João Herminio Martins Da Silva, Alex E. Clark, Jair L. Siqueira-Neto, Alexander L. Perryman, Glaucius Oliva, Sean Ekins, Carolina Horta Andrade:
Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. 6825-6843 - Brandon Úsuga-Acevedo, Yadiris García, Carola F. Díaz, Verónica A. Jiménez:
Rational Discovery of Microtubule-Stabilizing Peptides. 6844-6856
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