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ORCIDJournal of Chemical Information and Modeling, Volume 59
Volume 59, Number 1, January 2019
- Thanh-Hoang Nguyen-Vo
, Tri Le, Duy Pham, Tri Nguyen, Phuc Le, An Nguyen, Thanh Nguyen, Thien-Ngan Nguyen, Vu Nguyen, Hai Do, Khang Trinh, Trong Hai Duong, Ly Le:
VIETHERB: A Database for Vietnamese Herbal Species. 1-9 - Mahendra Awale, Jean-Louis Reymond:
Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning. 10-17 - Aoxiang Tao, Yuying Huang, Yasuhiro Shinohara, Matthew L. Caylor, Srinath Pashikanti, Dong Xu:
ezCADD: A Rapid 2D/3D Visualization-Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. 18-24 - Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimír Sládek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta:
Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations. 25-30 - Thomas Kainrad, Sascha Hunold, Thomas Seidel, Thierry Langer:
LigandScout Remote: A New User-Friendly Interface for HPC and Cloud Resources. 31-37 - Ying Yang, Amr H. Mahmoud, Markus A. Lill:
Modeling of Halogen-Protein Interactions in Co-Solvent Molecular Dynamics Simulations. 38-42 - Seokho Kang, Kyunghyun Cho:
Conditional Molecular Design with Deep Generative Models. 43-52 - Junmei Wang, Yubin Ge, Xiang-Qun Xie:
Development and Testing of Druglike Screening Libraries. 53-65 - Ruihan Zhang, Jing Lin, Yan Zou, Xing-Jie Zhang, Weilie Xiao:
Chemical Space and Biological Target Network of Anti-Inflammatory Natural Products. 66-73 - Fernanda I. Saldívar-González, Marilia Valli, Adriano D. Andricopulo, Vanderlan da Silva Bolzani, José L. Medina-Franco:
Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization. 74-85 - Michael González-Durruthy, Silvana Manske Nunes, Juliane Ventura-Lima, Marcos A. Gelesky, Humberto González Díaz, José Maria Monserrat, Riccardo Concu, M. Natália Dias Soeiro Cordeiro:
MitoTarget Modeling Using ANN-Classification Models Based on Fractal SEM Nano-Descriptors: Carbon Nanotubes as Mitochondrial F0F1-ATPase Inhibitors. 86-97 - Matthew P. Seddon, David A. Cosgrove, Martin J. Packer, Valerie J. Gillet:
Alignment-Free Molecular Shape Comparison Using Spectral Geometry: The Framework. 98-116 - Ruifeng Liu, Hao Wang, Kyle P. Glover, Michael G. Feasel, Anders Wallqvist:
Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure-Activity Relationship Models Based on Deep Neural Networks? 117-126 - Antoine Charpentier, David Mignon, Sophie Barbe, Juan Cortés, Thomas Schiex, Thomas Simonson, David Allouche:
Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems. 127-136 - Lucianna Helene Santos, Birgit J. Waldner, Julian E. Fuchs, Glaécia A. N. Pereira, Klaus R. Liedl, Ernesto Raúl Caffarena, Rafaela Salgado Ferreira:
Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. 137-148 - Andrea N. Bootsma, Steven E. Wheeler:
Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments. 149-158 - Shuheng Huang, Duo Zhang, Hu Mei, Muliadiyeremia Kevin, Sujun Qu, Xianchao Pan, Laichun Lu:
SMD-Based Interaction-Energy Fingerprints Can Predict Accurately the Dissociation Rate Constants of HIV-1 Protease Inhibitors. 159-169 - Lingling Zhang, Jianfen Fan, Mengnan Qu:
MD Simulations on the Transport Behaviors of Mixed Na+ and Li+ in a Transmembrane Cyclic Peptide Nanotube under an Electric Field. 170-180 - Ruifeng Liu, Anders Wallqvist:
Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds. 181-189 - Stavros Chatzieleftheriou, Stefanos Anogiannakis, Doros N. Theodorou, Nikos D. Lagaros:
SimNano: A Trust Region Strategy for Large-Scale Molecular Systems Energy Minimization Based on Exact Second-Order Derivative Information. 190-205 - Antoine Marion, Hatice Gokcan, Gerald Monard:
Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package. 206-214 - Fang-Yu Lin, Alexander D. MacKerell Jr.:
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. 215-228 - Kristian Kríz, Jan Rezác:
Reparametrization of the COSMO Solvent Model for Semiempirical Methods PM6 and PM7. 229-235 - Callum J. Dickson, Viktor Hornak, Dallas Bednarczyk, José S. Duca:
Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules. 236-244 - Stefan M. Ivanov, Roland G. Huber, Irfan Alibay, Jim Warwicker, Peter J. Bond:
Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway. 245-261 - Ernesto Quintas-Sánchez, Richard Dawes:
AUTOSURF: A Freely Available Program To Construct Potential Energy Surfaces. 262-271 - Xiao Liu, Long Peng, John Z. H. Zhang:
Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants. 272-281 - Shengchao Liu, Moayad Alnammi, Spencer S. Ericksen, Andrew F. Voter, Gene E. Ananiev, James L. Keck, F. Michael Hoffmann, Scott A. Wildman, Anthony Gitter:
Practical Model Selection for Prospective Virtual Screening. 282-293 - Jagna Witek, Shuzhe Wang, Benjamin Schroeder, Robin Lingwood, Andreas Dounas, Hans-Jörg Roth, Marianne Fouché, Markus Blatter, Oliver Lemke, Bettina G. Keller, Sereina Riniker:
Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. 294-308 - Srinivasaraghavan Kannan, Daniel Shao-Weng Tan, Chandra Shekhar Verma:
Effects of Single Nucleotide Polymorphisms on the Binding of Afatinib to EGFR: A Potential Patient Stratification Factor Revealed by Modeling Studies. 309-315 - Lanxuan Liu, Shuobing Fan, Wenjuan Li, Wentao Tao, Ting Shi, Yi-Lei Zhao:
Theoretical Investigation of the Structural Characteristics in the Active State of Akt1 Kinase. 316-325 - Subramani Karthikeyan, Ganesan Bharanidharan, Sriram Ragavan, Saravanan Kandasamy, Shanmugavel Chinnathambi, Kanniyappan Udayakumar, Rajendiran Mangaiyarkarasi, Anandh Sundaramoorthy, Prakasarao Aruna, Singaravelu Ganesan:
Comparative Binding Analysis ofN-Acetylneuraminic Acid in Bovine Serum Albumin and Human α-1 Acid Glycoprotein. 326-338 - Cheng-Dong Li, Muhammad Junaid, Hui Chen, Arif Ali, Dong-Qing Wei:
Helix-Switch Enables C99 Dimer Transition between the Multiple Conformations. 339-350 - Angelo Spinello, Elena Vecile, Antonio Abbate, Aldo Dobrina, Alessandra Magistrato:
How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways? 351-359 - Ping Xie, Si-Kao Guo, Hong Chen:
ATP-Concentration- and Force-Dependent Chemomechanical Coupling of Kinesin Molecular Motors. 360-372 - Khuraijam Dhanachandra Singh, Hamiyet Unal, Russell Desnoyer, Sadashiva S. Karnik:
Mechanism of Hormone Peptide Activation of a GPCR: Angiotensin II Activated State of AT1R Initiated by van der Waals Attraction. 373-385 - Philipp Nicolas Depta, Uwe Jandt, Maksym Dosta, An-Ping Zeng, Stefan Heinrich:
Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method. 386-398 - Zhicheng Zuo, Jin Liu:
Assessing the Performance of the Nonbonded Mg2+ Models in a Two-Metal-Dependent Ribonuclease. 399-408 - Ruxi Qi, Ray Luo:
Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. 409-420 - Dimas Suárez, Natalia Díaz:
Affinity Calculations of Cyclodextrin Host-Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods. 421-440 - Laia Julió Plana, Alejandro D. Nadra, Dario A. Estrin, F. Javier Luque, Luciana Capece:
Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. 441-452 - Zheng Zhao, Lei Xie, Philip E. Bourne:
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. 453-462 - Francois Berenger, Yoshihiro Yamanishi:
A Distance-Based Boolean Applicability Domain for Classification of High Throughput Screening Data. 463-476 - Alexios Koutsoukas, George Chang, Christopher E. Keefer:
In-Silico Extraction of Design Ideas Using MMPA-by-QSAR and its Application on ADME Endpoints. 477-485 - Youyi Peng, Hiep Dong, William J. Welsh:
Comprehensive 3D-QSAR Model Predicts Binding Affinity of Structurally Diverse Sigma 1 Receptor Ligands. 486-497 - Muhammad Junaid, Muhammad Tahir Khan, Shaukat Iqbal Malik, Dong-Qing Wei:
Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N. 498-508 - Jonas Dittrich, Denis Schmidt, Christopher Pfleger, Holger Gohlke:
Converging a Knowledge-Based Scoring Function: DrugScore2018. 509-521 - Ting Ran, Wenjuan Li, Bingling Peng, Binglan Xie, Tao Lu, Shuai Lu, Wen Liu:
Virtual Screening with a Structure-Based Pharmacophore Model to Identify Small-Molecule Inhibitors of CARM1. 522-534 - Doris A. Schuetz, Mattia Bernetti, Martina Bertazzo, Djordje Musil, Hans-Michael Eggenweiler, Maurizio Recanatini, Matteo Masetti, Gerhard F. Ecker, Andrea Cavalli:
Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. 535-549 - Majid Jafari, Farahnoosh Doustdar, Faramarz Mehrnejad:
Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles. 550-563 - Iuri Casciuc, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Jürgen Bajorath, Alexandre Varnek:
Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? 564-572 - Viet-Khoa Tran-Nguyen, Franck Da Silva, Guillaume Bret, Didier Rognan:
All in One: Cavity Detection, Druggability Estimate, Cavity-Based Pharmacophore Perception, and Virtual Screening. 573-585 - Domenico Alberga, Daniela Trisciuzzi, Michele Montaruli, Francesco Leonetti, Giuseppe Felice Mangiatordi, Orazio Nicolotti:
A New Approach for Drug Target and Bioactivity Prediction: The Multifingerprint Similarity Search Algorithm (MuSSeL). 586-596 - Xiaoli An, Shaoyong Lu, Kun Song, Qiancheng Shen, Meilan Huang, Xiaojun Yao, Huanxiang Liu, Jian Zhang:
Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? 597-604 - Alexander S. Kirpich, Mukundan Ragavan, James A. Bankson, Lauren M. McIntyre, Matthew E. Merritt:
Kinetic Analysis of Hepatic Metabolism Using Hyperpolarized Dihydroxyacetone. 605-614 - Li Xue, Bin Tang, Wei Chen, Jiesi Luo:
Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network. 615-624
Volume 59, Number 2, February 2019
- Aleksandra I. Jarmolinska, Qin Zhou, Joanna I. Sulkowska, Faruck Morcos:
DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings. 625-629 - Chen-Yang Jia, Fan Wang, Ge-Fei Hao, Guangfu Yang:
InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules. 630-635 - Johannes Heidrich, Thomas E. Exner, Frank M. Boeckler:
Predicting the Magnitude of σ-Holes Using VmaxPred, a Fast and Efficient Tool Supporting the Application of Halogen Bonds in Drug Discovery. 636-643 - Niek van Hilten, Florent Chevillard, Peter Kolb:
Virtual Compound Libraries in Computer-Assisted Drug Discovery. 644-651 - Qi Qi, Masahiko Taniguchi, Jonathan S. Lindsey:
Heuristics from Modeling of Spectral Overlap in Förster Resonance Energy Transfer (FRET). 652-667 - Lara Kuhnke, Antonius ter Laak, Andreas H. Göller:
Mechanistic Reactivity Descriptors for the Prediction of Ames Mutagenicity of Primary Aromatic Amines. 668-672 - Javier L. Baylon, Nicholas A. Cilfone, Jeffrey R. Gulcher, Thomas W. Chittenden:
Enhancing Retrosynthetic Reaction Prediction with Deep Learning Using Multiscale Reaction Classification. 673-688 - Benjamin P. Brown, Jeffrey L. Mendenhall, Jens Meiler:
BCL: : MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping. 689-701 - David A. Dreier, Nancy D. Denslow, Christopher J. Martyniuk:
Computational in Vitro Toxicology Uncovers Chemical Structures Impairing Mitochondrial Membrane Potential. 702-712 - Alexey Lagunin, Athina Geronikaki, Phaedra Eleftheriou, Pavel V. Pogodin, Alexey V. Zakharov:
Rational Use of Heterogeneous Data in Quantitative Structure-Activity Relationship (QSAR) Modeling of Cyclooxygenase/Lipoxygenase Inhibitors. 713-730 - Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey:
Conformator: A Novel Method for the Generation of Conformer Ensembles. 731-742 - Rasmus Leth, Bogac Ercig, Lars Olsen, Flemming Steen Jørgensen:
Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants. 743-753 - Joel Wahl, Martin Smiesko:
Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules. 754-765 - Thi Chinh Ngo, Thi Hau Nguyen, Duy Quang Dao:
Radical Scavenging Activity of Natural-Based Cassaine Diterpenoid Amides and Amines. 766-776 - Xiaoyan Zhou, Fangqiang Zhu:
Calculating Single-Channel Permeability and Conductance from Transition Paths. 777-785 - Tiago M. C. Simões, Abel João Padrão Gomes:
CavVis - A Field-of-View Geometric Algorithm for Protein Cavity Detection. 786-796 - Silvestre Massimo Modestia, Matheus Malta de Sá, Eric Auger, Gustavo Henrique Goulart Trossini, José Eduardo Krieger, Carlota de Oliveira Rangel-Yagui:
Biased Agonist TRV027 Determinants in AT1R by Molecular Dynamics Simulations. 797-808 - Rodrigo Cossio-Pérez, Gustavo Pierdominici-Sottile, Pablo Sobrado, Juliana Palma:
Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. 809-817 - Stefano Della-Longa, Alessandro Arcovito:
Microswitches for the Activation of the Nociceptin Receptor Induced by Cebranopadol: Hints from Microsecond Molecular Dynamics. 818-831 - Ge Qu, Mingxing Fu, Lili Zhao, Beibei Liu, Pi Liu, Wenchao Fan, Jun-An Ma, Zhoutong Sun:
Computational Insights into the Catalytic Mechanism of Bacterial Carboxylic Acid Reductase. 832-841 - Ye Jin, Mojie Duan, Xuwen Wang, Xiaotian Kong, Wenfang Zhou, Huiyong Sun, Hui Liu, Dan Li, Huidong Yu, Youyong Li, Tingjun Hou:
Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. 842-857 - Ning Tang, Budheswar Dehury, Kasper P. Kepp:
Computing the Pathogenicity of Alzheimer's Disease Presenilin 1 Mutations. 858-870 - Orkid Coskuner-Weber, Vladimir N. Uversky:
Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β42. 871-884 - Andreas Lange, Johannes Heidrich, Markus O. Zimmermann, Thomas E. Exner, Frank M. Boeckler:
Scaffold Effects on Halogen Bonding Strength. 885-894 - Minyi Su, Qifan Yang, Yu Du, Guoqin Feng, Zhihai Liu, Yan Li, Renxiao Wang:
Comparative Assessment of Scoring Functions: The CASF-2016 Update. 895-913 - Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu:
Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. 914-923 - Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. 924-930 - Theodore L. Fobe, Andrei F. Kazakov, Demian Riccardi:
Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank. 931-943 - Bing Xie, John D. Clark, David D. L. Minh:
Correction to "Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles". 944
Volume 59, Number 3, March 2019
- Günter Klambauer, Sepp Hochreiter, Matthias Rarey:
Machine Learning in Drug Discovery. 945-946 - Jochen Sieg, Florian Flachsenberg, Matthias Rarey:
In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. 947-961 - Noé Sturm, Jiangming Sun, Yves Vandriessche, Andreas Mayr, Günter Klambauer, Lars Carlsson, Ola Engkvist, Hongming Chen:
Application of Bioactivity Profile-Based Fingerprints for Building Machine Learning Models. 962-972 - Lixia Sun, Hongbin Yang, Yingchun Cai, Weihua Li, Guixia Liu, Yun Tang:
In Silico Prediction of Endocrine Disrupting Chemicals Using Single-Label and Multilabel Models. 973-982 - Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath:
Exploring Alternative Strategies for the Identification of Potent Compounds Using Support Vector Machine and Regression Modeling. 983-992 - Tomoyuki Miyao, Kimito Funatsu, Jürgen Bajorath:
Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction. 993-1004 - Yadi Zhou, Suntara Cahya, Steven A. Combs, Christos A. Nicolaou, Ji-Bo Wang, Prashant V. Desai, Jie Shen:
Exploring Tunable Hyperparameters for Deep Neural Networks with Industrial ADME Data Sets. 1005-1016 - Joshua Staker, Kyle Marshall, Robert Abel, Carolyn McQuaw:
Molecular Structure Extraction from Documents Using Deep Learning. 1017-1029 - Conrad Stork, Ya Chen, Martin Sícho, Johannes Kirchmair:
Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. 1030-1043 - Xiuming Li, Xin Yan, Qiong Gu, Huihao Zhou, Di Wu, Jun Xu:
DeepChemStable: Chemical Stability Prediction with an Attention-Based Graph Convolution Network. 1044-1049 - Nobuaki Yasuo, Masakazu Sekijima:
Improved Method of Structure-Based Virtual Screening via Interaction-Energy-Based Learning. 1050-1061 - Sergey Sosnin, Dmitry Karlov, Igor V. Tetko, Maxim V. Fedorov:
Comparative Study of Multitask Toxicity Modeling on a Broad Chemical Space. 1062-1072 - Chuipu Cai, Pengfei Guo, Yadi Zhou, Jingwei Zhou, Qi Wang, Fengxue Zhang, Jiansong Fang, Feixiong Cheng:
Deep Learning-Based Prediction of Drug-Induced Cardiotoxicity. 1073-1084 - Yingchun Cai, Hongbin Yang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
Computational Prediction of Site of Metabolism for UGT-Catalyzed Reactions. 1085-1095 - Nathan Brown, Marco Fiscato, Marwin H. S. Segler, Alain C. Vaucher:
GuacaMol: Benchmarking Models for de Novo Molecular Design. 1096-1108 - Deyani Nocedo-Mena, Carlos Cornelio, María del Rayo Camacho-Corona, Elvira Garza-González, Noemi Waksman de Torres, Sonia Arrasate, Nuria Sotomayor, Esther Lete, Humberto González Díaz:
Modeling Antibacterial Activity with Machine Learning and Fusion of Chemical Structure Information with Microorganism Metabolic Networks. 1109-1120 - Eleni E. Litsa, Matthew I. Peña, Mark Moll, George Giannakopoulos, George N. Bennett, Lydia E. Kavraki:
Machine Learning Guided Atom Mapping of Metabolic Reactions. 1121-1135 - Peter Pogány, Navot Arad, Sam Genway, Stephen D. Pickett:
De Novo Molecule Design by Translating from Reduced Graphs to SMILES. 1136-1146 - Stephanie A. Brocke, Alexandra Degen, Alexander D. MacKerell Jr., Bercem Dutagaci, Michael Feig:
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. 1147-1162 - Markus Hofmarcher, Elisabeth Rumetshofer, Djork-Arné Clevert, Sepp Hochreiter, Günter Klambauer:
Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks. 1163-1171 - José Jiménez, Davide Sabbadin, Alberto Cuzzolin, Gerard Martínez-Rosell, Jacob Gora, John Manchester, José S. Duca, Gianni De Fabritiis:
PathwayMap: Molecular Pathway Association with Self-Normalizing Neural Networks. 1172-1181 - Boris Sattarov, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Esben Jannik Bjerrum, Alexandre Varnek:
De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping. 1182-1196 - Thomas M. Whitehead, Benedict W. J. Irwin, Peter A. Hunt, Matthew D. Segall, Gareth John Conduit:
Imputation of Assay Bioactivity Data Using Deep Learning. 1197-1204 - Miha Skalic, José Jiménez, Davide Sabbadin, Gianni De Fabritiis:
Shape-Based Generative Modeling for de Novo Drug Design. 1205-1214 - Suqing Zheng, Wenping Chang, Wenxin Liu, Guang Liang, Yong Xu, Fu Lin:
Computational Prediction of a New ADMET Endpoint for Small Molecules: Anticommensal Effect on Human Gut Microbiota. 1215-1220 - Antonius P. A. Janssen, Sebastian H. Grimm, Ruud H. M. Wijdeven, Eelke B. Lenselink, Jacques Neefjes, Constant A. A. van Boeckel, Gerard J. P. van Westen, Mario van der Stelt:
Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes. 1221-1229 - Rubén Buendía, Thierry Kogej, Ola Engkvist, Lars Carlsson, Henrik Linusson, Ulf Johansson, Paolo Toccaceli, Ernst Ahlberg:
Accurate Hit Estimation for Iterative Screening Using Venn-ABERS Predictors. 1230-1237 - Mauro S. Nogueira, Oliver Koch:
The Development of Target-Specific Machine Learning Models as Scoring Functions for Docking-Based Target Prediction. 1238-1252 - Jan Wenzel, Hans Matter, K. Friedemann Schmidt:
Predictive Multitask Deep Neural Network Models for ADME-Tox Properties: Learning from Large Data Sets. 1253-1268 - Isidro Cortés-Ciriano, Andreas Bender:
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks. 1269-1281
Volume 59, Number 4, April 2019
- Maozi Chen, Yankang Jing, Lirong Wang, Zhiwei Feng, Xiang-Qun Xie:
DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. 1283-1289 - Seyed Hossein Jamali, Ludger Wolff, Tim M. Becker, Mariëtte de Groen, Mahinder Ramdin, Remco Hartkamp, André Bardow, Thijs J. H. Vlugt, Othonas A. Moultos:
OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-n Algorithm in LAMMPS. 1290-1294 - Lars P. E. Yunker, Sofia Donnecke, Michelle Ting, Darien Yeung, J. Scott McIndoe:
PythoMS: A Python Framework To Simplify and Assist in the Processing and Interpretation of Mass Spectrometric Data. 1295-1300 - Michael T. Humbert, Yong Zhang, Edward J. Maginn:
PyLAT: Python LAMMPS Analysis Tools. 1301-1305 - Michael Fernández, Fuqiang Ban, Godwin Woo, Olexandr Isayev, Carl Perez, Valery Fokin, Alexander Tropsha, Artem Cherkasov:
Quantitative Structure-Price Relationship (QS$R) Modeling and the Development of Economically Feasible Drug Discovery Projects. 1306-1313 - Tobias Fehlmann, Michael C. Hutter:
Conservation and Relevance of Pharmacophore Point Types. 1314-1323 - Robert P. Sheridan:
Interpretation of QSAR Models by Coloring Atoms According to Changes in Predicted Activity: How Robust Is It? 1324-1337 - Samuel T. Hutchinson, Rika Kobayashi:
Solvent-Specific Featurization for Predicting Free Energies of Solvation through Machine Learning. 1338-1346 - Mahendra Awale, Finton Sirockin, Nikolaus Stiefl, Jean-Louis Reymond:
Drug Analogs from Fragment-Based Long Short-Term Memory Generative Neural Networks. 1347-1356 - Robert A. Hoyt, Matthew M. Montemore, Ioanna Fampiou, Wei Chen, Georgios A. Tritsaris, Efthimios Kaxiras:
Machine Learning Prediction of H Adsorption Energies on Ag Alloys. 1357-1365 - Joshua T. Horton, Alice E. A. Allen, Leela S. Dodda, Daniel J. Cole:
QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics. 1366-1381 - Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy:
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. 1382-1397 - Said Tighadouini, Smaail Radi, Farid Abrigach, Redouane Benabbes, Driss Eddike, Monique Tillard:
Novel β-keto-enol Pyrazolic Compounds as Potent Antifungal Agents. Design, Synthesis, Crystal Structure, DFT, Homology Modeling, and Docking Studies. 1398-1409 - Carlos Garcia-Hernandez, Alberto Fernández, Francesc Serratosa:
Ligand-Based Virtual Screening Using Graph Edit Distance as Molecular Similarity Measure. 1410-1421 - Auradee Punkvang, Pharit Kamsri, Adrian J. Mulholland, James Spencer, Supa Hannongbua, Pornpan Pungpo:
Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-Dehydroshikimate and NADPH Suggest Strategies for MtbSDH Inhibition. 1422-1433 - Arslan R. Shaimardanov, Dmitry A. Shulga, Vladimir A. Palyulin:
Iterative Solvers for Empirical Partial Atomic Charges: Breaking the Curse of Cubic Numerical Complexity. 1434-1443 - Mayk C. Ramos, Vitor A. C. Horta, Bruno A. C. Horta:
Molecular Dynamics Simulations of PAMAM and PPI Dendrimers Using the GROMOS-Compatible 2016H66 Force Field. 1444-1457 - Rafael Ramis, Joaquín Ortega-Castro, Rodrigo Casasnovas, Laura Mariño, Bartolomé Vilanova, Miquel Angel Mestre Adrover, Juan Frau:
A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein. 1458-1471 - Laurent Hoffer, Magali Saez-Ayala, Dragos Horvath, Alexandre Varnek, Xavier Morelli, Philippe Roche:
CovaDOTS: In Silico Chemistry-Driven Tool to Design Covalent Inhibitors Using a Linking Strategy. 1472-1485 - Ingrid Grenet, Kevin Merlo, Jean-Paul Comet, Romain Tertiaux, David Rouquié, Frédéric Dayan:
Stacked Generalization with Applicability Domain Outperforms Simple QSAR on in Vitro Toxicological Data. 1486-1496 - Abhishek Kumar, Debaditya Mukherjee, Priyadarshi Satpati:
Mutations in Parkinson's Disease Associated Protein DJ-1 Alter the Energetics of DJ-1 Dimerization. 1497-1507 - Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z. H. Zhang:
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks. 1508-1514 - Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu:
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. 1515-1528 - Minh N. Nguyen, Neeladri Sen, Meiyin Lin, Thomas Leonard Joseph, Candida Vaz, Vivek Tanavde, Luke Way, Ted R. Hupp, Chandra S. Verma, M. S. Madhusudhan:
Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin. 1529-1546 - Edoardo Jun Mattioli, Andrea Bottoni, Matteo Calvaresi:
DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1. 1547-1553 - Fei Hu, Xiao-Ting Liu, Ji-Long Zhang, Qing-Chuan Zheng, Roberts I. Eglitis, Hong-Xing Zhang:
MD Simulation Investigation on the Binding Process of Smoke-Derived Germination Stimulants to Its Receptor. 1554-1562 - Ankan Gupta, Jaladhi Brahmbhatt, Raulia Syrlybaeva, Catherine Bodnar, Natalia Bodnar, Robert Bongard, Phani Raj Pokkuluri, Daniel S. Sem, Ramani Ramchandran, Rajendra Rathore, Marat R. Talipov:
Role of Conserved Histidine and Serine in the HCXXXXXRS Motif of Human Dual-Specificity Phosphatase 5. 1563-1574 - Yang Liu, Weifeng Li, Mary B. Chan-Park, Yuguang Mu:
The Necessity of d-Thr in the New Antibiotic Teixobactin: A Molecular Dynamics Study. 1575-1583 - Ashfaq Ur Rehman, Muhammad Tahir Khan, Hao Liu, Abdul Wadood, Shaukat Iqbal Malik, Hai-Feng Chen:
Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 ofMycobacterium tuberculosis. 1584-1597 - Ulf Norinder, Fredrik Svensson:
Multitask Modeling with Confidence Using Matrix Factorization and Conformal Prediction. 1598-1604 - Hsin-Yi Chen, Jian-Qiang Chen, Jun-Yan Li, Hung-Jin Huang, Xi Chen, Hao-Ying Zhang, Calvin Yu-Chian Chen:
Deep Learning and Random Forest Approach for Finding the Optimal Traditional Chinese Medicine Formula for Treatment of Alzheimer's Disease. 1605-1623 - Yonghui Chen, Tianqi Liu, Qiumu Xi, Wenqiang Jia, Dali Yin, Xiaojian Wang:
A Computational Approach to the Study of the Binding Mode of S1P1R Agonists Based on the Active-Like Receptor Model. 1624-1633 - Michael L. Drummond, Christopher I. Williams:
In Silico Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application. 1634-1644 - Angela Lopez-del Rio, Alfons Nonell-Canals, David Vidal, Alexandre Perera-Lluna:
Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning. 1645-1657 - Shuo Yin, Biao Zhang, Yang Yang, Yan Huang, Hong-Bin Shen:
Clustering Enhancement of Noisy Cryo-Electron Microscopy Single-Particle Images with a Network Structural Similarity Metric. 1658-1667 - Chun-Chun Wang, Xing Chen, Jia Qu, Ya-Zhou Sun, Jian-Qiang Li:
RFSMMA: A New Computational Model to Identify and Prioritize Potential Small Molecule-MiRNA Associations. 1668-1679 - Benjamin D. Sellers, Natalie C. James, Alberto Gobbi:
Correction to "A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments". 1680 - Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia:
Correction to "NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit". 1681
Volume 59, Number 5, May 2019
- Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
A Celebration of Women in Computational Chemistry. 1683-1692 - Georgia B. McGaughey, Rebecca Swett, Sara Swift, Ewa I. Chudyk, Kathryn Wong:
A Brief Recent History of Women in Computational Chemistry at Vertex Pharmaceuticals. 1693-1696 - Doriana Levré, Chiara Arcisto, Valentina Mercalli, Alberto Massarotti:
ZINClick v.18: Expanding Chemical Space of 1, 2, 3-Triazoles. 1697-1702 - Sridhar Neelamraju, David J. Wales, Shachi Gosavi:
Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins. 1703-1708 - Johanna M. Jansen, Gianfranco De Pascale, Susan Fong, Mika Lindvall, Heinz E. Moser, Keith Pfister, Bob Warne, Charles A. Wartchow:
Biased Complement Diversity Selection for Effective Exploration of Chemical Space in Hit-Finding Campaigns. 1709-1714 - Vasundhara Gadiyaram, Smitha Vishveshwara, Saraswathi Vishveshwara:
From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. 1715-1727 - Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer:
Advances and Challenges in Computational Target Prediction. 1728-1742 - Maud Chan-Yao-Chong, Dominique Durand, Tâp Ha-Duong:
Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. 1743-1758 - Beatrice Pecoraro, Marco Tutone, Ewelina Hoffman, Victoria Hutter, Anna Maria Almerico, Matthew Traynor:
Predicting Skin Permeability by Means of Computational Approaches: Reliability and Caveats in Pharmaceutical Studies. 1759-1771 - Tomasz Pienko, Joanna Trylska:
Computational Methods Used to Explore Transport Events in Biological Systems. 1772-1781 - Birgit Strodel, Orkid Coskuner-Weber:
Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. 1782-1805 - Stepan Stepanovic, Matija Zlatar, Marcel Swart, Maja Gruden:
The Irony of Manganocene: An Interplay between the Jahn-Teller Effect and Close-Lying Electronic and Spin States. 1806-1810 - Alzbeta Türková, Sankalp Jain, Barbara Zdrazil:
Integrative Data Mining, Scaffold Analysis, and Sequential Binary Classification Models for Exploring Ligand Profiles of Hepatic Organic Anion Transporting Polypeptides. 1811-1825 - Lennard Böselt, Dominik Sidler, Tobias Kittelmann, Jürgen Stohner, Daniel Zindel, Trixie Wagner, Sereina Riniker:
Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. 1826-1838 - Francesca Grisoni, Viviana Consonni, Davide Ballabio:
Machine Learning Consensus To Predict the Binding to the Androgen Receptor within the CoMPARA Project. 1839-1848 - Wenze Li, Wei Miao, Jingxia Cui, Chao Fang, Shunting Su, Hongzhi Li, Li Hong Hu, Yinghua Lu, Guanhua Chen:
Efficient Corrections for DFT Noncovalent Interactions Based on Ensemble Learning Models. 1849-1857 - Wafa M. Al-Madhagi, Najihah Mohd. Hashim, Nasser A. Awadh Ali, Hairin Taha, Abeer A. Alhadi, Adib A. Abdullah, Olla Sharhan, Rozana Othman:
Bioassay-Guided Isolation and in Silico Study of Antibacterial Compounds From Petroleum Ether Extract of Peperomia blanda (Jacq.) Kunth. 1858-1872 - Roger D. Amos, Rika Kobayashi:
Feature Engineering for Materials Chemistry - Does Size Matter? 1873-1881 - Konstantina Karathanou, Ana-Nicoleta Bondar:
Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor. 1882-1896 - Paulette A. Greenidge, Marcel J. J. Blommers, John P. Priestle, Jürg Hunziker:
How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection. 1897-1908 - Shuangyan Zhou, Yongchang Zhu, Xiaojun Yao, Huanxiang Liu:
Carbon Nanoparticles Inhibit the Aggregation of Prion Protein as Revealed by Experiments and Atomistic Simulations. 1909-1918 - Jun Pei, Zheng Zheng, Kenneth M. Merz Jr.:
Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection. 1919-1929 - Afshan Mohajeri, Akbar Omidvar, Hengameh Setoodeh:
Fine Structural Tuning of Thieno[3, 2-b] Pyrrole Donor for Designing Banana-Shaped Semiconductors Relevant to Organic Field Effect Transistors. 1930-1945 - Senem Avaz Seven, Oguzhan Oguz, Yusuf Ziya Menceloglu, Canan Atilgan:
Tuning Interaction Parameters of Thermoplastic Polyurethanes in a Binary Solvent To Achieve Precise Control over Microphase Separation. 1946-1956 - Victoria T. Lim, Christopher I. Bayly, Laszlo Fusti-Molnar, David L. Mobley:
Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid. 1957-1964 - Fuhui Zhang, Yuan Yuan, Minghui Xiang, Yanzhi Guo, Menglong Li, Yijing Liu, Xuemei Pu:
Molecular Mechanism Regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer. 1965-1976 - Lisbeth Ravnkilde Kjølbye, Anne Laustsen, Mikkel Vestergaard, Xavier Periole, Leonardo De Maria, Allan Svendsen, Andrea Coletta, Birgit Schiøtt:
Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation. 1977-1987 - Zijian Qin, Yao Xi, Shengde Zhang, Guiping Tu, Aixia Yan:
Classification of Cyclooxygenase-2 Inhibitors Using Support Vector Machine and Random Forest Methods. 1988-2008 - Chenchen Hu, Teng Lu, Hongxia Guo:
Developing a Transferable Coarse-Grained Model for the Prediction of Thermodynamic, Structural, and Mechanical Properties of Polyimides at Different Thermodynamic State Points. 2009-2025 - Priti Roy, Brataraj Ghosh, Prathit Chatterjee, Neelanjana Sengupta:
Cosolvent Impurities in SWCNT Nanochannel Confinement: Length Dependence of Water Dynamics Investigated with Atomistic Simulations. 2026-2034 - Phani Ghanakota, Debarati DasGupta, Heather A. Carlson:
Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. 2035-2045 - Kelly L. Damm-Ganamet, Nidhi Arora, Stephane Becart, James P. Edwards, Alec D. Lebsack, Heather M. McAllister, Marina I. Nelen, Navin L. Rao, Lori Westover, John J. M. Wiener, Taraneh Mirzadegan:
Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry. 2046-2062 - Kara E. Ranaghan, Darya Shchepanovska, Simon J. Bennie, Narin Lawan, Stephen J. Macrae, Jolanta Zurek, Frederick R. Manby, Adrian J. Mulholland:
Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution. 2063-2078 - Chunxing Ren, Xiaoxia Li, Li Guo:
Chemical Insight on Decreased Sensitivity of CL-20/TNT Cocrystal Revealed by ReaxFF MD Simulations. 2079-2092 - Han Zhang, Wenjuan Jiang, Payal Chatterjee, Yun Lyna Luo:
Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking. 2093-2102 - Angelika Baranowska-Laczkowska, Krzysztof Z. Laczkowski, Berta Fernández:
The Role of Substituents in Optical Rotation of Oxiranes, Oxetanes, and Oxathietanes. 2103-2109 - Dong Zheng, Yuming Gu, Xiang Li, Lizhu Zhang, Wei Zhao, Jing Ma:
Hydrogen Bonding Promoted Tautomerism between Azo and Hydrazone Forms in Calcon with Multistimuli Responsiveness and Biocompatibility. 2110-2122 - Michal Chojecki, Dorota Rutkowska-Zbik, Tatiana Korona:
Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules - Theoretical Study. 2123-2140 - Maxwell Fulford, Matteo Salvalaglio, Carla Molteni:
DeepIce: A Deep Neural Network Approach To Identify Ice and Water Molecules. 2141-2149 - Fiona L. Kearns, Carrie Robart, M. Trent Kemp, Sai Lakshmana Vankayala, Brette M. Chapin, Eric V. Anslyn, H. Lee Woodcock III, Joseph D. Larkin:
Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid. 2150-2158 - Rakesh Parida, G. Naaresh Reddy, Arindam Chakraborty, Santanab Giri, Madhurima Jana:
A New Class of Superhalogen Based Anion Receptor in Li-Ion Battery Electrolytes. 2159-2164 - Amartya Bose, Nancy Makri:
Quasiclassical Correlation Functions from the Wigner Density Using the Stability Matrix. 2165-2174 - Celina Sikorska:
Magnesium-Based Oxyfluoride Superatoms: Design, Structure, and Electronic Properties. 2175-2189 - Xiaohong Zhang, Ryan S. DeFever, Sapna Sarupria, Rachel B. Getman:
Free Energies of Catalytic Species Adsorbed to Pt(111) Surfaces under Liquid Solvent Calculated Using Classical and Quantum Approaches. 2190-2198 - Helena W. Qi, Heather J. Kulik:
Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis. 2199-2211 - Goar Sánchez-Sanz, Cristina Trujillo:
Cyclohexane-Based Scaffold Molecules Acting as Anion Transport, Anionophores, via Noncovalent Interactions. 2212-2217 - Jozica Dolenc, Wilfred F. van Gunsteren, Andrea E. Prota, Michel O. Steinmetz, John H. Missimer:
Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data. 2218-2230 - Arumugam Adilakshmi, Madhu Deepan Kumar, Madhavan Jaccob, Venkatachalam Tamilmani:
Theoretical Investigation of Steric Effect Influence on Reactivity of Substituted Butadienes with Bromocyclobutenone. 2231-2241 - Michelle A. Hunter, Julia M. T. A. Fischer, Marlies Hankel, Qinghong Yuan, Debra J. Searles:
Doping Effects on the Performance of Paired Metal Catalysts for the Hydrogen Evolution Reaction. 2242-2247 - Haizhen Liu, Liping Liu, Yan Fu, Erbao Liu, Bingchun Xue:
Theoretical Design of D-π-A-A Sensitizers with Narrow Band Gap and Broad Spectral Response Based on Boron Dipyrromethene for Dye-Sensitized Solar Cells. 2248-2256 - Miroslava Nedyalkova, Sergio Madurga, Marek Tobiszewski, Vasil Simeonov:
Calculating the Partition Coefficients of Organic Solvents in Octanol/Water and Octanol/Air. 2257-2263 - Jeffrey R. Wagner, Özlem Demir, Michael A. Carpenter, Hideki Aihara, Daniel A. Harki, Reuben S. Harris, Rommie E. Amaro:
Determinants of Oligonucleotide Selectivity of APOBEC3B. 2264-2273 - Sarmistha Majumdar, Debadrita Basu, Shubhra Ghosh Dastidar:
Conformational States of E7010 Is Complemented by Microclusters of Water Inside the α, β-Tubulin Core. 2274-2286 - Nandhitha Subramanian, Alexandra Schumann-Gillett, Alan E. Mark, Megan L. O'Mara:
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. 2287-2298 - Ekaterina D. Kots, Maria G. Khrenova, Alexander V. Nemukhin:
Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase. 2299-2308 - Ying Wang, Baichun Hu, Yusheng Peng, Xin Xiong, Wenhua Jing, Jian Wang, Huiyuan Gao:
In Silico Exploration of the Molecular Mechanism of Cassane Diterpenoids on Anti-inflammatory and Immunomodulatory Activity. 2309-2323 - Hong Zhang, Haohao Fu, Xueguang Shao, François Dehez, Christophe Chipot, Wensheng Cai:
Changes in Microenvironment Modulate the B- to A-DNA Transition. 2324-2330 - Xiuzhen Gao, Qinyuan Ma, Meiling Chen, Miaomiao Dong, Zhongji Pu, Xianhai Zhang, Yuanda Song:
Insight into the Highly Conserved and Differentiated Cofactor-Binding Sites ofmeso-Diaminopimelate Dehydrogenase StDAPDH. 2331-2338 - Brittney L. Worrell, Anne M. Brown, Webster L. Santos, David R. Bevan:
In Silico Characterization of Structural Distinctions between Isoforms of Human and Mouse Sphingosine Kinases for Accelerating Drug Discovery. 2339-2351 - Burak T. Kaynak, Pemra Doruker:
Protein-Ligand Complexes as Constrained Dynamical Systems. 2352-2358 - Jingwei Weng, Wenning Wang:
Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis. 2359-2366 - Jack Fuller, Tim R. Wilson, Mark E. Eberhart, Anastassia N. Alexandrova:
Charge Density in Enzyme Active Site as a Descriptor of Electrostatic Preorganization. 2367-2373 - Meng Wu, Liping Sun, Qingtong Zhou, Yao Peng, Zhijie Liu, Suwen Zhao:
Molecular Mechanism of Acetate Transport through the Acetate Channel SatP. 2374-2382 - Kimberly R. Sabsay, Rebecca T. Lee, Leandre M. Ravatt, Javin P. Oza, Ashley Ringer McDonald:
Computational Models for Activated Human MEK1: Identification of Key Active Site Residues and Interactions. 2383-2393 - Giulia Palermo:
Structure and Dynamics of the CRISPR-Cas9 Catalytic Complex. 2394-2406 - Jayangika N. Dahanayake, Elaheh Shahryari, Kirsten M. Roberts, Micah E. Heikes, Chandana Kasireddy, Katie R. Mitchell-Koch:
Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. 2407-2422 - Erica Modeste, Lily Mawby, Bill R. Miller III, Eugene Y. Wu, Carol A. Parish:
A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart. 2423-2431 - Nadia Elghobashi-Meinhardt:
Computational Tools Unravel Putative Sterol Binding Sites in the Lysosomal NPC1 Protein. 2432-2441 - Mare Oja, Sulev Sild, Uko Maran:
Logistic Classification Models for pH-Permeability Profile: Predicting Permeability Classes for the Biopharmaceutical Classification System. 2442-2455 - Claudia Llinas del Torrent, Nil Casajuana-Martin, Leonardo Pardo, Gary Tresadern, Laura Pérez-Benito:
Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. 2456-2466 - Katarina Kores, Samo Lesnik, Urban Bren, Dusanka Janezic, Janez Konc:
Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. 2467-2478 - Cristina Trujillo, Aoife Flood, Goar Sánchez-Sanz, Brendan Twamley, Isabel Rozas:
Planarity or Nonplanarity: Modulating Guanidine Derivatives as α2-Adrenoceptors Ligands. 2479-2486 - Yie-Vern Lee, Sy Bing Choi, Habibah A. Wahab, Theam Soon Lim, Yee-Siew Choong:
Applications of Ensemble Docking in Potential Inhibitor Screening forMycobacterium tuberculosisIsocitrate Lyase Using a Local Plant Database. 2487-2495 - Karolina Mikulska-Ruminska, Indira Shrivastava, James Krieger, She Zhang, Hongchun Li, Hülya Bayir, Sally E. Wenzel, Andrew P. Vandemark, Valerian E. Kagan, Ivet Bahar:
Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. 2496-2508
Volume 59, Number 6, June 2019
- Jian Wang, Nikolay V. Dokholyan:
MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. 2509-2515 - Ramil I. Nugmanov, Ravil N. Mukhametgaleev, Tagir Akhmetshin, Timur Gimadiev, Valentina A. Afonina, Timur I. Madzhidov, Alexandre Varnek:
CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing. 2516-2521 - Stephan Schott-Verdugo, Holger Gohlke:
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building. 2522-2528 - Connor W. Coley, William H. Green Jr., Klavs F. Jensen:
RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application. 2529-2537 - Pravin Ambure, Amit Kumar Halder, Humberto González Díaz, M. Natália Dias Soeiro Cordeiro:
QSAR-Co: An Open Source Software for Developing Robust Multitasking or Multitarget Classification-Based QSAR Models. 2538-2544 - Adam C. Mater, Michelle L. Coote:
Deep Learning in Chemistry. 2545-2559 - Robert Schmidt, Emanuel S. R. Ehmki, Farina Ohm, Hans-Christian Ehrlich, Andriy Mashychev, Matthias Rarey:
Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. 2560-2571 - Emanuel S. R. Ehmki, Robert Schmidt, Farina Ohm, Matthias Rarey:
Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. 2572-2586 - Jos L. Teunissen, Frank De Proft, Freija De Vleeschouwer:
Acceleration of Inverse Molecular Design by Using Predictive Techniques. 2587-2599 - Jean-Paul Ebejer, Paul W. Finn, Wing Ki Wong, Charlotte M. Deane, Garrett M. Morris:
Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening. 2600-2616 - Wesley Beckner, Jim Pfaendtner:
Fantastic Liquids and Where To Find Them: Optimizations of Discrete Chemical Space. 2617-2625 - Tomoyuki Miyao, Kimito Funatsu:
Iterative Screening Methods for Identification of Chemical Compounds with Specific Values of Various Properties. 2626-2641 - Dai Feng, Vladimir Svetnik, Andy Liaw, Matthew T. Pratola, Robert P. Sheridan:
Building Quantitative Structure-Activity Relationship Models Using Bayesian Additive Regression Trees. 2642-2655 - Shunsuke Tamura, Tomoyuki Miyao, Kimito Funatsu:
Development of R-Group Fingerprints Based on the Local Landscape from an Attachment Point of a Molecular Structure. 2656-2663 - Vasilios Duros, Jonathan Grizou, Abhishek Sharma, S. Hessam M. Mehr, Andrius Bubliauskas, Przemyslaw Frei, Haralampos N. Miras, Leroy Cronin:
Intuition-Enabled Machine Learning Beats the Competition When Joint Human-Robot Teams Perform Inorganic Chemical Experiments. 2664-2671 - Mark A. Watson, Haoyu S. Yu, Art D. Bochevarov:
Generation of Tautomers Using Micro-pKa's. 2672-2689 - E. Prabhu Raman:
Template-Based Method for Conformation Generation and Scoring for Congeneric Series of Ligands. 2690-2701 - Jithin Vachery, Sayan Ranu:
RISC: Rapid Inverted-Index Based Search of Chemical Fingerprints. 2702-2713 - Xiao Hu, Alessandro Contini:
Rescoring Virtual Screening Results with the MM-PBSA Methods: Beware of Internal Dielectric Constants. 2714-2728 - Francesca Moraca, Ana Negri, Cesar de Oliveira, Robert Abel:
Application of Free Energy Perturbation (FEP+) to Understanding Ligand Selectivity: A Case Study to Assess Selectivity Between Pairs of Phosphodiesterases (PDE's). 2729-2740 - Robert Sinclair, Peter V. Coveney:
Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold. 2741-2745 - Federico Iacovelli, Kevin Cabungcal Hernandez, Alessandro Desideri, Mattia Falconi:
Probing the Functional Topology of a pH-Dependent Triple Helix DNA Nanoswitch Family through Gaussian Accelerated MD Simulation. 2746-2752 - Gianmarc Grazioli, Saswata Roy, Carter T. Butts:
Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines. 2753-2764 - Roman G. Efremov:
Dielectric-Dependent Strength of Interlipid Hydrogen Bonding in Biomembranes: Model Case Study. 2765-2775 - Alexander D. Wade, Andrea Rizzi, Yuanqing Wang, David J. Huggins:
Computational Fluorine Scanning Using Free-Energy Perturbation. 2776-2784 - Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
Building of Robust and Interpretable QSAR Classification Models by Means of the Rivality Index. 2785-2804 - Antonio-Jesús Banegas-Luna, José Pedro Cerón-Carrasco, Savíns Puertas-Martín, Horacio Pérez Sánchez:
BRUSELAS: HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases. 2805-2817 - David Schaller, Szymon Pach, Gerhard Wolber:
PyRod: Tracing Water Molecules in Molecular Dynamics Simulations. 2818-2829 - Giulio Mattedi, Francesca Deflorian, Jonathan S. Mason, Chris de Graaf, Francesco L. Gervasio:
Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. 2830-2836 - Seung Soo Kim, Young Min Rhee:
Modeling Charge Flux by Interpolating Atomic Partial Charges. 2837-2849 - Srinivasaraghavan Kannan, Stephen J. Fox, Chandra S. Verma:
Exploring Gatekeeper Mutations in EGFR through Computer Simulations. 2850-2858 - Elnaz Aledavood, Gleiciane Moraes, Jerônimo Lameira, Ana Castro, F. Javier Luque, Carolina Estarellas:
Understanding the Mechanism of Direct Activation of AMP-Kinase: Toward a Fine Allosteric Tuning of the Kinase Activity. 2859-2870 - Xiaojing Cong, Jean-Baptiste Chéron, Jérôme Golebiowski, Serge Antonczak, Sébastien Fiorucci:
Allosteric Modulation Mechanism of the mGluR5 Transmembrane Domain. 2871-2878 - Prabir Khatua, Souvik Mondal, Sanjoy Bandyopadhyay:
Effects of Metal Ions on Aβ42 Peptide Conformations from Molecular Simulation Studies. 2879-2893 - Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary:
HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo. 2894-2899 - Nick Matthews, Akio Kitao, Stephen D. Laycock, Steven Hayward:
Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. 2900-2912 - Abhishek Thakur, Joan M. Hevel, Orlando Acevedo:
Examining Product Specificity in Protein Arginine Methyltransferase 7 (PRMT7) Using Quantum and Molecular Mechanical Simulations. 2913-2923 - Lei Liu, Stephen Chan, Tianlu Mo, Wei Ding, Shaoning Yu, Qi Zhang, Shuguang Yuan:
Movements of the Substrate-Binding Clamp of Cypemycin Decarboxylase CypD. 2924-2929 - Ida Ritacco, Angelo Spinello, Emiliano Ippoliti, Alessandra Magistrato:
Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme. 2930-2940 - Wanlei Wei, Jiaying Luo, Jérôme Waldispühl, Nicolas Moitessier:
Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. 2941-2951 - Satoshi Ono, Matthew R. Naylor, Chad E. Townsend, Chieko Okumura, Okimasa Okada, R. Scott Lokey:
Conformation and Permeability: Cyclic Hexapeptide Diastereomers. 2952-2963 - Jacob D. Bowman, William H. Coldren, Steffen Lindert:
Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations. 2964-2972 - Francesca Vasile, Guido Tiana:
Determination of Structural Ensembles of Flexible Molecules in Solution from NMR Data Undergoing Spin Diffusion. 2973-2979 - Xiaohui Wang, Zhaoxi Sun:
Determination of Base-Flipping Free-Energy Landscapes from Nonequilibrium Stratification. 2980-2994 - Agnieszka Krzeminska, Katarzyna Swiderek:
Molecular Insights into the Substrate-Assisted Mechanism of Viral DNA 3′-End Processing in Intasome of Prototype Foamy Virus Integrase from Molecular Dynamic and QM/MM Studies. 2995-3005 - Da Shi, Feroz Khan, Ruben Abagyan:
Extended Multitarget Pharmacology of Anticancer Drugs. 3006-3017 - Vincent D. Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, Alexander D. MacKerell Jr.:
Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. 3018-3035 - Antonio Llinàs, Alex Avdeef:
Solubility Challenge Revisited after Ten Years, with Multilab Shake-Flask Data, Using Tight (SD ∼ 0.17 log) and Loose (SD ∼ 0.62 log) Test Sets. 3036-3040 - D'artagnan Greene, Ruxi Qi, Remy Nguyen, Tianyin Qiu, Ray Luo:
Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies. 3041-3056 - Yi-Heng Zhu, Jun Hu, Xiaoning Song, Dong-Jun Yu:
DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines. 3057-3071 - J. Jesús Naveja, Dagmar Stumpfe, José L. Medina-Franco, Jürgen Bajorath:
Exploration of Target Synergy in Cancer Treatment by Cell-Based Screening Assay and Network Propagation Analysis. 3072-3079 - Xinxiang Wang, Sheng-You Huang:
Integrating Bonded and Nonbonded Potentials in the Knowledge-Based Scoring Function for Protein Structure Prediction. 3080-3090
Volume 59, Number 7, July 2019
- Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro:
Frontiers in CryoEM Modeling. 3091-3093 - Andrei L. Lomize, Jacob M. Hage, Kevin Schnitzer, Konstantin Golobokov, Mitchell B. Lafaive, Alexander C. Forsyth, Irina D. Pogozheva:
PerMM: A Web Tool and Database for Analysis of Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. 3094-3099 - André Fischer, Martin Smiesko:
Ligand Pathways in Nuclear Receptors. 3100-3109 - Ruimin Ma, Zeyu Liu, Quanwei Zhang, Zhiyu Liu, Tengfei Luo:
Evaluating Polymer Representations via Quantifying Structure-Property Relationships. 3110-3119 - J. César Cruz, Raymundo Hernández-Esparza, Álvaro Vázquez-Mayagoitia, Rubicelia Vargas, Jorge Garza:
Implementation of the Molecular Electrostatic Potential over Graphics Processing Units. 3120-3127 - Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.:
Using AMBER18 for Relative Free Energy Calculations. 3128-3135 - Yuanxun Wang, Qiuyu Fu, Yu Zhou, Yunfei Du, Niu Huang:
Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions. 3136-3143 - Jorge Alberto Cerecedo-Cordoba, Juan Javier González Barbosa, Juan Frausto Solís, Nohra Violeta Gallardo-Rivas:
Melting Temperature Estimation of Imidazole Ionic Liquids with Clustering Methods. 3144-3153 - Nenad B. Krdzavac, Sebastian Mosbach, Daniel Nurkowski, Philipp Buerger, Jethro Akroyd, Jacob Martin, Angiras Menon, Markus Kraft:
An Ontology and Semantic Web Service for Quantum Chemistry Calculations. 3154-3165 - Niclas Ståhl, Göran Falkman, Alexander Karlsson, Gunnar Mathiason, Jonas Boström:
Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design. 3166-3176 - Stefano Costanzi, Austin Cohen, Abigail Danfora, Marjan Dolatmoradi:
Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β2 Adrenergic Receptor as a Case Study. 3177-3190 - Felipe Zapata, Lars Ridder, Johan Hidding, Christoph R. Jacob, Ivan Infante, Lucas Visscher:
QMflows: A Tool Kit for Interoperable Parallel Workflows in Quantum Chemistry. 3191-3197 - Andrei L. Lomize, Irina D. Pogozheva:
Physics-Based Method for Modeling Passive Membrane Permeability and Translocation Pathways of Bioactive Molecules. 3198-3213 - Antonio Vitale, Velia Minicozzi:
Monitoring Insulin-Aggregated Structures in the Presence of Epigallocatechin-3-gallate and Melatonin by Molecular Dynamics Simulations. 3214-3221 - Xin-Qiu Yao, Mohamed Momin, Donald Hamelberg:
Establishing a Framework of Using Residue-Residue Interactions in Protein Difference Network Analysis. 3222-3228 - Ashfaq Ur Rehman, Humaira Rafiq, Mueed Ur Rahman, Jiayi Li, Hao Liu, Shenggan Luo, Taaha Arshad, Abdul Wadood, Hai-Feng Chen:
Gain-of-Function SHP2 E76Q Mutant Rescuing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia. 3229-3239 - Chunlai Feng, Hengwei Chen, Xianqin Yuan, Mengqiu Sun, Kexin Chu, Hanqing Liu, Mengjie Rui:
Gene Expression Data Based Deep Learning Model for Accurate Prediction of Drug-Induced Liver Injury in Advance. 3240-3250 - Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi:
Computational Model To Predict the Fraction of Unbound Drug in the Brain. 3251-3261 - Reza Talandashti, Hamid Mahdiuni, Majid Jafari, Faramarz Mehrnejad:
Molecular Basis for Membrane Selectivity of Antimicrobial Peptide Pleurocidin in the Presence of Different Eukaryotic and Prokaryotic Model Membranes. 3262-3276 - Peng Ding, Ziyang Chen, Hao Chen, Zizhen Zhang, Zhihong Liu, Xin Yan, Huihao Zhou, Qiong Gu, Chanjuan Li, Jun Xu:
Structurally Selective Mechanism of Liver X Receptor Ligand: In Silico and In Vitro Studies. 3277-3290 - Duc Duy Nguyen, Guo-Wei Wei:
AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening. 3291-3304 - Jun Pei, Zheng Zheng, Hyunji Kim, Lin Frank Song, Sarah Walworth, Margaux R. Merz, Kenneth M. Merz Jr.:
Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection. 3305-3315 - Mohan R. Pradhan, Minh N. Nguyen, Srinivasaraghavan Kannan, Stephen J. Fox, Chee Keong Kwoh, David P. Lane, Chandra S. Verma:
Characterization of Hydration Properties in Structural Ensembles of Biomolecules. 3316-3329 - Isidro Cortés-Ciriano, Andreas Bender:
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout. 3330-3339 - Liang-Yong Xia, Ziyi Yang, Hui Zhang, Yong Liang:
Improved Prediction of Drug-Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization. 3340-3351
Volume 59, Number 8, August 2019
- Zhaoqiang Chen, Xinben Zhang, Cheng Peng, Jinan Wang, Zhijian Xu, Kaixian Chen, Jiye Shi, Weiliang Zhu:
D3Pockets: A Method and Web Server for Systematic Analysis of Protein Pocket Dynamics. 3353-3358 - Athina Meletiou, James Gebbie-Rayet, Charles A. Laughton:
Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application. 3359-3364 - Viivi H. A. Hirvonen, Katharine Hammond, Ewa I. Chudyk, Michael A. L. Limb, James Spencer, Adrian J. Mulholland, Marc van der Kamp:
An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases. 3365-3369 - Kevin Yang, Kyle Swanson, Wengong Jin, Connor W. Coley, Philipp Eiden, Hua Gao, Angel Guzman-Perez, Timothy Hopper, Brian Kelley, Miriam Mathea, Andrew Palmer, Volker Settels, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay:
Analyzing Learned Molecular Representations for Property Prediction. 3370-3388 - Zhijian Xu, Qian Zhang, Jiye Shi, Weiliang Zhu:
Underestimated Noncovalent Interactions in Protein Data Bank. 3389-3399 - Martin Sícho, Conrad Stork, Angelica Mazzolari, Christina de Bruyn Kops, Alessandro Pedretti, Bernard Testa, Giulio Vistoli, Daniel Svozil, Johannes Kirchmair:
FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes. 3400-3412 - Andrea N. Bootsma, Steven E. Wheeler:
Converting SMILES to Stacking Interaction Energies. 3413-3421 - Zhijie Liu, Suresh B. Singh, Yajun Zheng, Peter Lindblom, Colin Tice, Chengguo Dong, Linghang Zhuang, Yi Zhao, Barbara A. Kruk, Deepak Lala, David A. Claremon, Gerard M. McGeehan, Richard D. Gregg, Robert Cain:
Discovery of Potent Inhibitors of 11β-Hydroxysteroid Dehydrogenase Type 1 Using a Novel Growth-Based Protocol of in Silico Screening and Optimization in CONTOUR. 3422-3436 - Antonija Tomic, Gordan Horvat, Michael Ramek, Dejan Agic, Hrvoje Brkic, Sanja Tomic:
New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. 3437-3453 - Agnieszka Brzyska, Krzysztof Wolinski:
Isomerization and Decomposition of 2-Methylfuran with External Forces. 3454-3463 - Rodrigo Ochoa, Alessandro Laio, Pilar Cossio:
Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. 3464-3473 - Bishnu Thapa, Krishnan Raghavachari:
Energy Decomposition Analysis of Protein-Ligand Interactions Using Molecules-in-Molecules Fragmentation-Based Method. 3474-3484 - Raimondas Galvelis, Stefan Doerr, João M. Damas, Matt J. Harvey, Gianni De Fabritiis:
A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning. 3485-3493 - Misaela Francisco-Marquez, Annia Galano:
Detailed Investigation of the Outstanding Peroxyl Radical Scavenging Activity of Two Novel Amino-Pyridinol-Based Compounds. 3494-3505 - Damien Monet, Nathan Desdouits, Michael Nilges, Arnaud Blondel:
mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics. 3506-3518 - Vladimir P. Berishvili, Valentin O. Perkin, Andrew E. Voronkov, Eugene V. Radchenko, Riyaz Syed, Venkata Ramana Reddy Chittireddy, Viness Pillay, Pradeep Kumar, Yahya E. Choonara, Ahmed Kamal, Vladimir A. Palyulin:
Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors. 3519-3532 - Tatsuya Yamada, Tomohiko Hayashi, Simon Hikiri, Naohiro Kobayashi, Hiroshi Yanagawa, Mitsunori Ikeguchi, Masato Katahira, Takashi Nagata, Masahiro Kinoshita:
How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2? 3533-3544 - German P. Barletta, Gisela R. Franchini, Betina Córsico, Sebastian Fernandez Alberti:
Fatty Acid and Retinol-Binding Protein: Unusual Protein Conformational and Cavity Changes Dictated by Ligand Fluctuations. 3545-3555 - Ren Kong, Feng Wang, Jian Zhang, Fengfei Wang, Shan Chang:
CoDockPP: A Multistage Approach for Global and Site-Specific Protein-Protein Docking. 3556-3564 - Ferruccio Palazzesi, Marc A. Grundl, Alexander Pautsch, Alexander Weber, Christofer S. Tautermann:
A Fast Ab Initio Predictor Tool for Covalent Reactivity Estimation of Acrylamides. 3565-3571 - Juan Pablo Arcon, Lucas A. Defelipe, Elias D. López, Osvaldo Burastero, Carlos P. Modenutti, Xavier Barril, Marcelo A. Marti, Adrian Gustavo Turjanski:
Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening. 3572-3583 - Sami T. Kurkinen, Sakari Lätti, Olli T. Pentikäinen, Pekka A. Postila:
Getting Docking into Shape Using Negative Image-Based Rescoring. 3584-3599
Volume 59, Number 9, September 2019
- Thereza A. Soares, Habibah A. Wahab:
Molecular Simulation in Latin America: Coming of Age. 3601-3602 - W. Patrick Walters, Renxiao Wang:
New Trends in Virtual Screening. 3603-3604 - Holger Kruse, Jirí Sponer, Pascal Auffinger:
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis". 3605-3608 - Helena W. Qi, Heather J. Kulik:
Reply to "Comment on 'Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis'". 3609-3610 - Florian Koensgen, Franck Da Silva, Didier Rognan, Esther Kellenberger:
Unsupervised Classification of G-Protein Coupled Receptors and Their Conformational States Using IChem Intramolecular Interaction Patterns. 3611-3618 - Chongze Zhao, Xi Dai, Yecheng Li, Qingqing Guo, Jianhua Zhang, Xiaotong Zhang, Ling Wang:
EK-DRD: A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge. 3619-3624 - David de Sancho, Anne Aguirre:
MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics. 3625-3629 - Neil J. Bruce, Gaurav K. Ganotra, Stefan Richter, Rebecca C. Wade:
KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding. 3630-3634 - Olga A. Tarasova, Nadezhda Yu. Biziukova, Dmitry Filimonov, Vladimir Poroikov, Marc C. Nicklaus:
Data Mining Approach for Extraction of Useful Information About Biologically Active Compounds from Publications. 3635-3644 - Eric Walker, Joshua Kammeraad, Jonathan Goetz, Michael T. Robo, Ambuj Tewari, Paul M. Zimmerman:
Learning To Predict Reaction Conditions: Relationships between Solvent, Molecular Structure, and Catalyst. 3645-3654 - Yunierkis Pérez-Castillo, Stellamaris Sotomayor-Burneo, Karina Beatriz Jimenes Vargas, Mario Salvador González-Rodríguez, Maykel Cruz-Monteagudo, Vinicio Armijos-Jaramillo, M. Natália Dias Soeiro Cordeiro, Fernanda Borges, Aminael Sánchez-Rodríguez, Eduardo Tejera:
CompScore: Boosting Structure-Based Virtual Screening Performance by Incorporating Docking Scoring Function Components into Consensus Scoring. 3655-3666 - Tao Zeng, Zhihong Liu, Huawei Liu, Wengan He, Xiaowen Tang, Liwei Xie, Ruibo Wu:
Exploring Chemical and Biological Space of Terpenoids. 3667-3678 - Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer:
Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints. 3679-3691 - Leigh Weston, Vahe Tshitoyan, John Dagdelen, Olga Kononova, Amalie Trewartha, Kristin A. Persson, Gerbrand Ceder, Anubhav Jain:
Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature. 3692-3702 - Hsuan-Hao Hsu, Chen-Hsuan Huang, Shiang-Tai Lin:
New Data Structure for Computational Molecular Design with Atomic or Fragment Resolution. 3703-3713 - Zi-Yi Yang, Zhi-Jiang Yang, Jie Dong, Liang-Liang Wang, Liu-Xia Zhang, Jun-Jie Ding, Xiao-Qin Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
Structural Analysis and Identification of Colloidal Aggregators in Drug Discovery. 3714-3726 - Atsushi Yoshimori, Yuichi Horita, Toru Tanoue, Jürgen Bajorath:
Method for Systematic Analogue Search Using the Mega SAR Matrix Database. 3727-3734 - Christoph Alexander Bauer:
How to Model Inter- and Intramolecular Hydrogen Bond Strengths with Quantum Chemistry. 3735-3743 - Suvamay Jana, Soumadwip Ghosh, Sanychen Muk, Benjamin Levy, Nagarajan Vaidehi:
Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. 3744-3754 - Zakaria Alamiddine, Balaji Selvam, Jérôme Graton, Adèle D. Laurent, Elodie Landagaray, Jacques Lebreton, Monique Mathé-Allainmat, Steeve H. Thany, Jean-Yves Le Questel:
Binding of Sulfoxaflor to Aplysia californica-AChBP: Computational Insights from Multiscale Approaches. 3755-3769 - Shoichi Tanimoto, Norio Yoshida, Tsuyoshi Yamaguchi, Seiichiro L. Ten-no, Haruyuki Nakano:
Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory. 3770-3781 - Kyle D. Konze, Pieter H. Bos, Markus K. Dahlgren, Karl Leswing, Ivan Tubert-Brohman, Andrea Bortolato, Braxton Robbason, Robert Abel, Sathesh Bhat:
Reaction-Based Enumeration, Active Learning, and Free Energy Calculations To Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin-Dependent Kinase 2 Inhibitors. 3782-3793 - Wei Jiang, Christophe Chipot, Benoît Roux:
Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD. 3794-3802 - Marina Macchiagodena, Marco Pagliai, Claudia Andreini, Antonio Rosato, Piero Procacci:
Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. 3803-3816 - Xiaofeng Wang, Zhen Li, Mingjian Jiang, Shuang Wang, Shugang Zhang, Zhiqiang Wei:
Molecule Property Prediction Based on Spatial Graph Embedding. 3817-3828 - Mark Z. Griffiths, Wataru Shinoda:
tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules. 3829-3838 - Shuo Zhou, Ziyuan Zhou, Kai Ding, Yaxia Yuan, Fang Zheng, Chang-Guo Zhan:
In Silico Observation of the Conformational Opening of the Glutathione-Binding Site of Microsomal Prostaglandin E2 Synthase-1. 3839-3845 - Süleyman Selim Çinaroglu, Emel Timuçin:
Comparative Assessment of Seven Docking Programs on a Nonredundant Metalloprotein Subset of the PDBbind Refined. 3846-3859 - Manuel I. Osorio, Ma. Angeles Cabrera, Fernando D. González Nilo, José M. Pérez-Donoso:
Odd Loop Regions of XenA and XenB Enzymes Modulate Their Interaction with Nitro-explosives Compounds and Provide Structural Support for Their Regioselectivity. 3860-3870 - Liping He, Jingxiao Bao, Yunpeng Yang, Suzhen Dong, Lujia Zhang, Yifei Qi, John Z. H. Zhang:
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning. 3871-3878 - Ai Niitsu, Suyong Re, Hiraku Oshima, Motoshi Kamiya, Yuji Sugita:
De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. 3879-3888 - Lijie Wang, Lin Zhang, Fufeng Liu, Yan Sun:
Molecular Energetics of Doxorubicin Pumping by Human P-Glycoprotein. 3889-3898 - Bo Wang, Junjie Zhang, Yinghao Wu:
A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2. 3899-3909 - Yang Zhou, Rongfeng Zou, Guanglin Kuang, Bengt Långström, Christer Halldin, Hans Ågren, Yaoquan Tu:
Enhanced Sampling Simulations of Ligand Unbinding Kinetics Controlled by Protein Conformational Changes. 3910-3918 - Ryuhei Harada, Yasuteru Shigeta:
Selection Rules for Outliers in Outlier Flooding Method Regulate Its Conformational Sampling Efficiency. 3919-3926 - Marco Montefiori, Simona Pilotto, Chiara Marabelli, Elisabetta Moroni, Mariarosaria Ferraro, Stefano A. Serapian, Andrea Mattevi, Giorgio Colombo:
Impact of Mutations on NPAC Structural Dynamics: Mechanistic Insights from MD Simulations. 3927-3937 - Passainte Ibrahim, David Wifling, Timothy Clark:
Universal Activation Index for Class A GPCRs. 3938-3945 - Yu-Ming Lee, Cédric Grauffel, Ting Chen, Karen Sargsyan, Carmay Lim:
Factors Governing the Different Functions of Zn2+-Sites with Identical Ligands in Proteins. 3946-3954 - Haoyu S. Yu, Cen Gao, Dmitry Lupyan, Yujie Wu, Takayuki Kimura, Chuanjie Wu, Leif D. Jacobson, Edward Harder, Robert Abel, Lingle Wang:
Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics. 3955-3967 - Yuchen Wang, Haichun Liu, Yuanrong Fan, Xingye Chen, Yan Yang, Lu Zhu, Junnan Zhao, Yadong Chen, Yanmin Zhang:
In Silico Prediction of Human Intravenous Pharmacokinetic Parameters with Improved Accuracy. 3968-3980 - Jaechang Lim, Seongok Ryu, Kyubyong Park, Yo Joong Choe, Jiyeon Ham, Woo Youn Kim:
Predicting Drug-Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation. 3981-3988 - Adrià Gil, Angel Sanchez-Gonzalez, Vicenç Branchadell:
Unraveling the Modulation of the Activity in Drugs Based on Methylated Phenanthroline When Intercalating between DNA Base Pairs. 3989-3995 - Shayma El-Atawneh, Shira Hirsch, Rivka Hadar, Joseph Tam, Amiram Goldblum:
Prediction and Experimental Confirmation of Novel Peripheral Cannabinoid-1 Receptor Antagonists. 3996-4006 - Jissy A. Kuriappan, Neil Osheroff, Marco de Vivo:
Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II. 4007-4017 - Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar, Daan P. Geerke:
A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation. 4018-4033 - Christian Kramer:
Nonadditivity Analysis. 4034-4042 - Yuko Tsuchiya, Kei Taneishi, Yasushige Yonezawa:
Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics. 4043-4051 - Jamie R. Nuñez, Sean M. Colby, Dennis G. Thomas, Malak M. Tfaily, Nikola Tolic, Elin M. Ulrich, Jon R. Sobus, Thomas O. Metz, Justin G. Teeguarden, Ryan S. Renslow:
Evaluation of In Silico Multifeature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. 4052-4060
Volume 59, Number 10, October 2019
- Giulia Palermo, Kira A. Armacost, Maria C. Nagan:
Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry. 4061-4062 - Yecheng Li, Chongze Zhao, Jianhua Zhang, Shiyang Zhai, Boyan Wei, Ling Wang:
HybridMolDB: A Manually Curated Database Dedicated to Hybrid Molecules for Chemical Biology and Drug Discovery. 4063-4069 - Pravin Ambure, Agnieszka Gajewicz-Skretna, M. Natália Dias Soeiro Cordeiro, Kunal Roy:
New Workflow for QSAR Model Development from Small Data Sets: Small Dataset Curator and Small Dataset Modeler. Integration of Data Curation, Exhaustive Double Cross-Validation, and a Set of Optimal Model Selection Techniques. 4070-4076 - Marco Foscato, Vishwesh Venkatraman, Vidar R. Jensen:
DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules. 4077-4082 - Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory A. Landrum, Andrea Volkamer:
TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows. 4083-4086 - Sayuri Pacheco, Jesse C. Kaminsky, Iurii K. Kochnev, Jacob D. Durrant:
PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. 4087-4092 - Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov:
Sharing Data from Molecular Simulations. 4093-4099 - Charuvaka Muvva, N. Arul Murugan, Venkata Surya Kumar Choutipalli, Venkatesan Subramanian:
Unraveling the Unbinding Pathways of Products Formed in Catalytic Reactions Involved in SIRT1-3: A Random Acceleration Molecular Dynamics Simulation Study. 4100-4115 - Gudong Li, Wei Li, Yuting Xie, Xiaobo Wan, Guojun Zheng, Niu Huang, Yu Zhou:
Discovery of Novel Pim-1 Kinase Inhibitors with a Flexible-Receptor Docking Protocol. 4116-4119 - José Pérez-Parras Toledano, Nicolás García-Pedrajas, Gonzalo Cerruela García:
Multilabel and Missing Label Methods for Binary Quantitative Structure-Activity Relationship Models: An Application for the Prediction of Adverse Drug Reactions. 4120-4130 - Wen Torng, Russ B. Altman:
Graph Convolutional Neural Networks for Predicting Drug-Target Interactions. 4131-4149 - Jin Zhang, Daniel Mucs, Ulf Norinder, Fredrik Svensson:
LightGBM: An Effective and Scalable Algorithm for Prediction of Chemical Toxicity-Application to the Tox21 and Mutagenicity Data Sets. 4150-4158 - Jia Ying Mi, Hong Lin Zhai, Bo Yin, Sha Sha Li, Shao Hua Lu:
Applications of Discrete Shmaliy Moments on the Quantitative Analysis of Multitarget Compounds Based on the Chemical Spectra. 4159-4166 - Gian Marco Ghiandoni, Michael J. Bodkin, Beining Chen, Dimitar Hristozov, James E. A. Wallace, James Webster, Valerie J. Gillet:
Development and Application of a Data-Driven Reaction Classification Model: Comparison of an Electronic Lab Notebook and Medicinal Chemistry Literature. 4167-4187 - Shruti Venkatram, Chiho Kim, Anand Chandrasekaran, Rampi Ramprasad:
Critical Assessment of the Hildebrand and Hansen Solubility Parameters for Polymers. 4188-4194 - Brajesh K. Rai, Vishnu Sresht, Qingyi Yang, Raymond J. Unwalla, Meihua Tu, Alan M. Mathiowetz, Gregory A. Bakken:
Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein-Ligand Complexes using ab Initio Calculations. 4195-4208 - Johannes R. Loeffler, Michael Schauperl, Klaus R. Liedl:
Hydration of Aromatic Heterocycles as an Adversary of π-Stacking. 4209-4219 - Angus Voice, Gary Tresadern, Herman van Vlijmen, Adrian J. Mulholland:
Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors. 4220-4227 - Kwang Hyun Cho, Seyoung Chung, Young Min Rhee:
Efficiently Transplanting Potential Energy Interpolation Database between Two Systems: Bacteriochlorophyll Case with FMO and LH2 Complexes. 4228-4238 - Shun Zhu:
Validation of the Generalized Force Fields GAFF, CGenFF, OPLS-AA, and PRODRGFF by Testing Against Experimental Osmotic Coefficient Data for Small Drug-Like Molecules. 4239-4247 - Simon Stephan, Monika Thol, Jadran Vrabec, Hans Hasse:
Thermophysical Properties of the Lennard-Jones Fluid: Database and Data Assessment. 4248-4265 - Henderson James Cleaves II, Christopher J. Butch, Pieter Buys Burger, Jay Goodwin, Markus Meringer:
One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. 4266-4277 - James L. McDonagh, Ardita Shkurti, David J. Bray, Richard L. Anderson, Edward O. Pyzer-Knapp:
Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields. 4278-4288 - Ran Sun, Zilong Li, Thomas C. Bishop:
TMB Library of Nucleosome Simulations. 4289-4299 - Angelo Felline, Luca Belmonte, Francesco Raimondi, Luca Bellucci, Francesca Fanelli:
Interconnecting Flexibility, Structural Communication, and Function in RhoGEF Oncoproteins. 4300-4313 - Ismail Erol, Bunyemin Cosut, Serdar Durdagi:
Toward Understanding the Impact of Dimerization Interfaces in Angiotensin II Type 1 Receptor. 4314-4327 - Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, Juan R. Perilla:
High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities. 4328-4338 - Hanjing Ding, Hui Liu:
Mapping the Binding Hot Spots on Human Programmed Cell Death 1 and Its Ligand with Free-Energy Simulations. 4339-4349 - Juan José Galano-Frutos, Javier Sancho:
Accurate Calculation of Barnase and SNase Folding Energetics Using Short Molecular Dynamics Simulations and an Atomistic Model of the Unfolded Ensemble: Evaluation of Force Fields and Water Models. 4350-4360 - Daniel Tietze, Desireé Kaufmann, Alesia A. Tietze, Andreas Voll, Raphael Reher, Gabriele M. König, Felix Hausch:
Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action. 4361-4373 - Lili Dong, Shengqiang Shen, Wei Chen, Dongdong Xu, Qing Yang, Huizhe Lu, Jianjun Zhang:
Discovery of Novel Inhibitors Targeting Human O-GlcNAcase: Docking-Based Virtual Screening, Biological Evaluation, Structural Modification, and Molecular Dynamics Simulation. 4374-4382 - Martin Kulke, Myriam Uhrhan, Norman Geist, Dorothea Brüggemann, Bastian Ohler, Walter Langel, Susan Köppen:
Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain. 4383-4392 - Chun-Gang Min, Qing-Bo Liu, Yan Leng, Carla M. Magalhães, Shao-Jun Huang, Chun-Xia Liu, Xi-Kun Yang, Luís Pinto Da Silva:
Mechanistic Insight into the Chemiluminescent Decomposition of Cypridina Dioxetanone and the Chemiluminescent, Fluorescent Properties of the Light Emitter of Cypridina Bioluminescence. 4393-4401 - Zhenyan Jiang, Hansi Zhang:
Molecular Mechanism of S1P Binding and Activation of the S1P1 Receptor. 4402-4412 - Nazar Ileri Ercan:
Understanding Interactions of Curcumin with Lipid Bilayers: A Coarse-Grained Molecular Dynamics Study. 4413-4426 - Sandip Mondal, Sanjoy Bandyopadhyay:
Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water. 4427-4437 - Jesse G. Meyer, Shengchao Liu, Ian J. Miller, Joshua J. Coon, Anthony Gitter:
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests. 4438-4449 - Eric J. Martin, Valery R. Polyakov, Xiang-Wei Zhu, Li Tian, Prasenjit Mukherjee, Xin Liu:
All-Assay-Max2 pQSAR: Activity Predictions as Accurate as Four-Concentration IC50s for 8558 Novartis Assays. 4450-4459 - Rama K. Mishra, Kristine K. Deibler, Matthew R. Clutter, Purav P. Vagadia, Matthew O'Connor, Gary E. Schiltz, Raymond Bergan, Karl A. Scheidt:
Modeling MEK4 Kinase Inhibitors through Perturbed Electrostatic Potential Charges. 4460-4466 - Xiangying Zhang, Hongbin Sun, Xiaoan Wen, Haoliang Yuan:
A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling. 4467-4474 - Maritza Hernandez, Guo Liang Gan, Kirby Linvill, Carl Dukatz, Jun Feng, Govinda Bhisetti:
A Quantum-Inspired Method for Three-Dimensional Ligand-Based Virtual Screening. 4475-4485 - Thérèse E. Malliavin, Antonio Mucherino, Carlile Lavor, Leo Liberti:
Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach. 4486-4503 - Tae-Geun Yu, Hak-Sung Kim, Yoonjoo Choi:
B-SIDER: Computational Algorithm for the Design of Complementary β-Sheet Sequences. 4504-4511
Volume 59, Number 11, November 2019
- Pavel V. Pogodin, Alexey Lagunin, Anastasia V. Rudik, Dmitry S. Druzhilovskiy, Dmitry Filimonov, Vladimir Poroikov:
AntiBac-Pred: A Web Application for Predicting Antibacterial Activity of Chemical Compounds. 4513-4518 - Henrique S. Fernandes, Sergio F. Sousa, Nuno M. F. S. A. Cerqueira:
VMD Store-A VMD Plugin to Browse, Discover, and Install VMD Extensions. 4519-4523 - Adolfo Bastida, Javier Carmona-García, Jose Zuñiga, Alberto Requena, Javier Cerezo:
Intraresidual Correlated Motions in Peptide Chains. 4524-4527 - Karim Abbasi, Antti Poso, Jahan B. Ghasemi, Massoud Amanlou, Ali Masoudi-Nejad:
Deep Transferable Compound Representation across Domains and Tasks for Low Data Drug Discovery. 4528-4539 - Jianing Lu, Xuben Hou, Cheng Wang, Yingkai Zhang:
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions. 4540-4549 - Tobias Lemke, Andrej Berg, Alok Jain, Christine Peter:
EncoderMap(II): Visualizing Important Molecular Motions with Improved Generation of Protein Conformations. 4550-4560 - Jiangpeng Wu, Jun Bai, Wei Wang, Lili Xi, Pengyi Zhang, Jingfeng Lan, Liansheng Zhang, Shuyan Li:
ATBdiscrimination: An in Silico Tool for Identification of Active Tuberculosis Disease Based on Routine Blood Test and T-SPOT.TB Detection Results. 4561-4568 - Dmitry V. Zankov, Timur I. Madzhidov, Asima I. Rakhimbekova, Timur Gimadiev, Ramil I. Nugmanov, Marina A. Kazymova, Igor I. Baskin, Alexandre Varnek:
Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules. 4569-4576 - Xiaoqi Shan, Xiangeng Wang, Cheng-Dong Li, Yanyi Chu, Yufang Zhang, Yi Xiong, Dong-Qing Wei:
Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method. 4577-4586 - Zhenxing Wu, Tailong Lei, Chao Shen, Zhe Wang, Dong-Sheng Cao, Tingjun Hou:
ADMET Evaluation in Drug Discovery. 19. Reliable Prediction of Human Cytochrome P450 Inhibition Using Artificial Intelligence Approaches. 4587-4601 - Qifan Yang, Minyi Su, Yan Li, Renxiao Wang:
Revisiting the Relationship Between Correlation Coefficient, Confidence Level, and Sample Size. 4602-4612 - Alexey V. Zakharov, Tongan Zhao, Dac-Trung Nguyen, Tyler Peryea, Timothy Sheils, Adam Yasgar, Ruili Huang, Noel Southall, Anton Simeonov:
Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models. 4613-4624 - Louis Bellmann, Patrick Penner, Matthias Rarey:
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. 4625-4635 - Xiangyu Zhang, Jing Cui, Kexin Zhang, Jiasheng Wu, Yongjin Lee:
Machine Learning Prediction on Properties of Nanoporous Materials Utilizing Pore Geometry Barcodes. 4636-4644 - Hongyao Zhu, Mark E. Flanagan, Robert V. Stanton:
Designing DNA Encoded Libraries of Diverse Products in a Focused Property Space. 4645-4653 - Ozlem Erdas-Cicek, Ali Osman Atac, A. Selen Gurkan-Alp, Erdem Buyukbingol, Ferda Nur Alpaslan:
Three-Dimensional Analysis of Binding Sites for Predicting Binding Affinities in Drug Design. 4654-4662 - Jason D. Boettger, James D. Kubicki:
Evaluating Computational Chemistry Methods for Isotopic Fractionation between CO2(g) and H2O(g). 4663-4677 - Simona De Vita, Gianluigi Lauro, Dafne Ruggiero, Stefania Terracciano, Raffaele Riccio, Giuseppe Bifulco:
Protein Preparation Automatic Protocol for High-Throughput Inverse Virtual Screening: Accelerating the Target Identification by Computational Methods. 4678-4690 - Hamed S. Hayatshahi, Emilio Ahuactzin, Peng Tao, Shouyi Wang, Jin Liu:
Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps. 4691-4705 - Yipin Lu, Shankara Anand, William A. Shirley, Peter Gedeck, Brian P. Kelley, Suzanne Skolnik, Stephane Rodde, Mai Nguyen, Mika K. Lindvall, Weiping Jia:
Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines. 4706-4719 - Huafeng Xu:
Optimal Measurement Network of Pairwise Differences. 4720-4728 - Irfan Alibay, Richard A. Bryce:
Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. 4729-4741 - Aini Palizhati, Wen Zhong, Kevin Tran, Seoin Back, Zachary W. Ulissi:
Toward Predicting Intermetallics Surface Properties with High-Throughput DFT and Convolutional Neural Networks. 4742-4749 - Candide Champion, Stephen J. Barigye, Wanlei Wei, Zhaomin Liu, Paul Labute, Nicolas Moitessier:
Atom Type Independent Modeling of the Conformational Energy of Benzylic, Allylic, and Other Bonds Adjacent to Conjugated Systems. 4750-4763 - Wanlei Wei, Candide Champion, Zhaomin Liu, Stephen J. Barigye, Paul Labute, Nicolas Moitessier:
Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence. 4764-4777 - Richard Marchese Robinson, Dawn Geatches, Chris Morris, Rebecca Mackenzie, Andrew G. P. Maloney, Kevin J. Roberts, Alexandru Moldovan, Ernest Chow, Klimentina Pencheva, Dinesh Ramesh Mirpuri Vatvani:
Evaluation of Force-Field Calculations of Lattice Energies on a Large Public Dataset, Assessment of Pharmaceutical Relevance, and Comparison to Density Functional Theory. 4778-4792 - Sheng Yang, Hao Liu, Yangpeng Zhang, Hui Lu, Hai-Feng Chen:
Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. 4793-4805 - Jens Reinisch, Michael Diedenhofen, Rainer Wilcken, Anikó Udvarhelyi, Andreas Glöß:
Benchmarking Different QM Levels for Usage with COSMO-RS. 4806-4813 - Benjamin P. Pritchard, Doaa Altarawy, Brett T. Didier, Tara D. Gibson, Theresa L. Windus:
New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community. 4814-4820 - Robert C. Harris, Jana Shen:
GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations. 4821-4832 - Xing-Rong Fan, Jinsha Huang, Rui Zhang, Fei Wang, Qiuyu Zhang, Guanlin Li, Jinyong Yan, Houjin Zhang, Yunjun Yan, Li Xu:
Convolution Neural Network-Based Prediction of Protein Thermostability. 4833-4843 - David A. Winkler, Andrew C. Warden, Thierry Prangé, N. Colloc'h, A. W. Thornton, J.-F. Ramirez-Gil, G. Farjot, I. Katz:
Massive in Silico Study of Noble Gas Binding to the Structural Proteome. 4844-4854 - Gábor Dániel Balogh, Tamás Gyöngyösi, István Timári, Mihály Herczeg, Anikó Borbás, Krisztina Fehér, Katalin E. Kövér:
Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides. 4855-4867 - Peter Husen, Claus Nielsen, Carlos F. Martino, Ilia A. Solov'yov:
Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein. 4868-4879 - Deepak Bandyopadhyay, Constantine Kreatsoulas, Pat G. Brady, Joseph Boyer, Zangdong He, Genaro Scavello, Tyler Peryea, Ajit Jadhav, Dac-Trung Nguyen, Rajarshi Guha:
Scaffold-Based Analytics: Enabling Hit-to-Lead Decisions by Visualizing Chemical Series Linked across Large Datasets. 4880-4892 - Sebastian Schneckener, Sergio Grimbs, Jessica Hey, Stephan Menz, Maren Osmers, Steffen Schaper, Alexander Hillisch, Andreas H. Göller:
Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters. 4893-4905 - Nicholas T. Cockroft, Xiaolin Cheng, James R. Fuchs:
STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. 4906-4920 - Krystel El Hage, Vincent Zoete:
Strong Enrichment of Aromatic and Sulfur-Containing Residues in Ligand-Protein Binding Sites. 4921-4928 - Ugo Bastolla, Yves Dehouck:
Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression. 4929-4941 - Nikhil Maroli, Naveen Kumar Kalagatur, Balu Bhasuran, Achuth Jayakrishnan, Renuka Ramalingam Manoharan, Ponmalai Kolandaivel, Jeyakumar Natarajan, Krishna Kadirvelu:
Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation. 4942-4958 - Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, Yun Tang:
Correction to "admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties". 4959
Volume 59, Number 12, December 2019
- Mattia Mori, Fabrizio Manetti, Bruno Botta, Andrea Tafi:
In Memory of Maurizio Botta: His Contribution to the Development of Computer-Aided Drug Design. 4961-4967 - Chris Bizon, Steven Cox, James P. Balhoff, Yaphet Kebede, Patrick Wang, Kenneth Morton, Karamarie Fecho, Alexander Tropsha:
ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. 4968-4973 - Damian Lesniak, Sabina Podlewska, Stanislaw Jastrzebski, Igor Sieradzki, Andrzej J. Bojarski, Jacek Tabor:
Development of New Methods Needs Proper Evaluation - Benchmarking Sets for Machine Learning Experiments for Class A GPCRs. 4974-4992 - Shi-Ping Peng, Yi Zhao:
Convolutional Neural Networks for the Design and Analysis of Non-Fullerene Acceptors. 4993-5001 - Minjian Yang, Bingzhong Tao, Chengjuan Chen, Wenqiang Jia, Shaolei Sun, Tiantai Zhang, Xiaojian Wang:
Machine Learning Models Based on Molecular Fingerprints and an Extreme Gradient Boosting Method Lead to the Discovery of JAK2 Inhibitors. 5002-5012 - Ghanshyam Pilania, Carl N. Iverson, Turab Lookman, Babetta L. Marrone:
Machine-Learning-Based Predictive Modeling of Glass Transition Temperatures: A Case of Polyhydroxyalkanoate Homopolymers and Copolymers. 5013-5025 - Shoichi Ishida, Kei Terayama, Ryosuke Kojima, Kiyosei Takasu, Yasushi Okuno:
Prediction and Interpretable Visualization of Retrosynthetic Reactions Using Graph Convolutional Networks. 5026-5033 - Thomas J. Summers, Baty P. Daniel, Qianyi Cheng, Nathan J. DeYonker:
Quantifying Inter-Residue Contacts through Interaction Energies. 5034-5044 - Christian Nowak, Mayank Misra, Fernando A. Escobedo:
Framework for Inverse Mapping Chemistry-Agnostic Coarse-Grained Simulation Models into Chemistry-Specific Models. 5045-5056 - Maximilian Kriebel, Matthias Hennemann, Frank R. Beierlein, Dana D. Medina, Thomas Bein, Timothy Clark:
Propagation of Holes and Electrons in Metal-Organic Frameworks. 5057-5064 - Guohui Wei, Xianjun Fu, Zhenguo Wang:
Multisolvent Similarity Measure of Chinese Herbal Medicine Ingredients for Cold-Hot Nature Identification. 5065-5073 - Jan Walther Perthold, Chris Oostenbrink:
GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations. 5074-5085 - Hong Li, Wenyou Zhu, Yongjun Liu:
Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes. 5086-5098 - Piers A. Townsend, Matthew N. Grayson:
Density Functional Theory Transition-State Modeling for the Prediction of Ames Mutagenicity in 1, 4 Michael Acceptors. 5099-5103 - Huihui Liu, Susumu Okazaki, Wataru Shinoda:
Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein. 5104-5110 - Christian J. Suess, Floriane L. Martins, Anna K. Croft, Christof M. Jäger:
Radical Stabilization Energies for Enzyme Engineering: Tackling the Substrate Scope of the Radical Enzyme QueE. 5111-5125 - Nootcharin Wasukan, Mayuso Kuno, Rawiwan Maniratanachote:
Molecular Docking as a Promising Predictive Model for Silver Nanoparticle-Mediated Inhibition of Cytochrome P450 Enzymes. 5126-5134 - Steffen Wolf, Marta Amaral, Maryse Lowinski, Francois Vallée, Djordje Musil, Jörn Güldenhaupt, Matthias K. Dreyer, Jörg Bomke, Matthias Frech, Jürgen Schlitter, Klaus Gerwert:
Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations. 5135-5147 - Carlos A. Ortiz-Mahecha, Hugo-Javier Bohórquez, William A. Agudelo, Manuel A. Patarroyo, Manuel-Elkin Patarroyo, Carlos F. Suárez:
Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal. 5148-5160 - Levente M. Mihalovits, György G. Ferenczy, György M. Keserü:
Catalytic Mechanism and Covalent Inhibition of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials. 5161-5173 - Bill Pham, Avery Bancroft Arons, Jeremy G. Vincent, Elias J. Fernandez, Tongye Shen:
Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions. 5174-5182 - Panagiotis Lagarias, Kerry Barkan, Eva Tzortzini, Margarita Stampelou, Eleni Vrontaki, Graham Ladds, Antonios Kolocouris:
Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis. 5183-5197 - Ryuhei Harada, Vladimír Sládek, Yasuteru Shigeta:
Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. 5198-5206 - Amy K. Smith, Elias Khayat, Christopher Lockhart, Dmitri K. Klimov:
Do Cholesterol and Sphingomyelin Change the Mechanism of Aβ25-35 Peptide Binding to Zwitterionic Bilayer? 5207-5217 - Hamid R. Kalhor, Mohammadparsa Jabbary:
Investigating Reliable Conditions for HEWL as an Amyloid Model in Computational Studies and Drug Interactions. 5218-5229 - Ning Tang, Thomas D. Sandahl, Peter Ott, Kasper P. Kepp:
Computing the Pathogenicity of Wilson's Disease ATP7B Mutations: Implications for Disease Prevalence. 5230-5243 - Xingye Chen, Haichun Liu, Wuchen Xie, Yan Yang, Yuchen Wang, Yuanrong Fan, Yi Hua, Lu Zhu, Junnan Zhao, Tao Lu, Yadong Chen, Yanmin Zhang:
Investigation of Crystal Structures in Structure-Based Virtual Screening for Protein Kinase Inhibitors. 5244-5262 - James M. B. McFarlane, Katherine D. Krause, Irina Paci:
Accelerated Structural Prediction of Flexible Protein-Ligand Complexes: The SLICE Method. 5263-5275 - Zhou Yin:
Mechanism of Small Molecules Inhibiting Activator Protein-1 DNA Binding Probed with Induced Fit Docking and Metadynamics Simulations. 5276-5280 - Chun-Chun Wang, Xing Chen:
A Unified Framework for the Prediction of Small Molecule-MicroRNA Association Based on Cross-Layer Dependency Inference on Multilayered Networks. 5281-5293 - Pratishtha Singh, Anjali D. Ganjiwale, Allyn C. Howlett, Sudha M. Cowsik:
Molecular Interaction between Distal C-Terminal Domain of the CB1 Cannabinoid Receptor and Cannabinoid Receptor Interacting Proteins (CRIP1a/CRIP1b). 5294-5303 - Kevin Yang, Kyle Swanson, Wengong Jin, Connor W. Coley, Philipp Eiden, Hua Gao, Angel Guzman-Perez, Timothy Hopper, Brian Kelley, Miriam Mathea, Andrew Palmer, Volker Settels, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay:
Correction to Analyzing Learned Molecular Representations for Property Prediction. 5304-5305
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