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Journal of Chemical Information and Modeling, Volume 60
Volume 60, Number 1, January 2020
- Kira A. Armacost
, Sereina Riniker
, Zoe Cournia
:
Novel Directions in Free Energy Methods and Applications. 1-5 - Francesca Peccati
:
NCIPLOT4 Guide for Biomolecules: An Analysis Tool for Noncovalent Interactions. 6-10 - Guanglei Cui
, Alan P. Graves
, Eric S. Manas:
GRAM: A True Null Model for Relative Binding Affinity Predictions. 11-16 - Congcong Gong
, Chuanli Hou, Maojin Yao
, Jiaoyan Ren
:
New Discoveries in Hybrid Orbitals to Characterize Molecules and Predict Biomolecular Interactions. 17-21 - Vadim Korolev
, Artem Mitrofanov
, Alexandru Korotcov, Valery Tkachenko:
Graph Convolutional Neural Networks as "General-Purpose" Property Predictors: The Universality and Limits of Applicability. 22-28 - Seung Hwan Hong
, Seongok Ryu, Jaechang Lim
, Woo Youn Kim
:
Molecular Generative Model Based on an Adversarially Regularized Autoencoder. 29-36 - Pingjian Ding
, Cong Shen
, Zihan Lai, Cheng Liang, Guanghui Li, Jiawei Luo:
Incorporating Multisource Knowledge To Predict Drug Synergy Based on Graph Co-regularization. 37-46 - Shuangjia Zheng
, Jiahua Rao, Zhongyue Zhang, Jun Xu
, Yuedong Yang
:
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. 47-55 - Vikram Sundar
, Lucy J. Colwell:
The Effect of Debiasing Protein-Ligand Binding Data on Generalization. 56-62 - Li Fu, Lu Liu, Zhi-Jiang Yang, Pan Li, Jun-Jie Ding, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. 63-76 - Yibo Li
, Jianxing Hu
, Yanxing Wang
, Jielong Zhou, Liangren Zhang, Zhenming Liu
:
DeepScaffold: A Comprehensive Tool for Scaffold-Based De Novo Drug Discovery Using Deep Learning. 77-91 - Yan Yang, Yanmin Zhang
, Yi Hua, Xingye Chen, Yuanrong Fan, Yuchen Wang, Li Liang, Chenglong Deng, Tao Lu, Yadong Chen
, Haichun Liu:
In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality. 92-107 - Feroz Farazi
, Jethro Akroyd
, Sebastian Mosbach
, Philipp Buerger, Daniel Nurkowski
, Maurin Salamanca
, Markus Kraft
:
OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms. 108-120 - Alice Capecchi, Alain Zhang, Jean-Louis Reymond
:
Populating Chemical Space with Peptides Using a Genetic Algorithm. 121-132 - Irene Luque Ruiz
, Miguel Ángel Gómez-Nieto
:
Building Highly Reliable Quantitative Structure-Activity Relationship Classification Models Using the Rivality Index Neighborhood Algorithm with Feature Selection. 133-151 - Tigran M. Abramyan
, Yi An, Dmitri Kireev
:
Off-Pocket Activity Cliffs: A Puzzling Facet of Molecular Recognition. 152-161 - Mengna Lin, Lin-Tai Da
:
Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry. 162-174 - Richard Mariadasse
, Sanjay Kumar Choubey, Jeyaraman Jeyakanthan
:
Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. 175-191 - Callum J. Dickson
, Camilo Velez-Vega, José S. Duca:
Revealing Molecular Determinants of hERG Blocker and Activator Binding. 192-203 - Nguyen Thanh Nguyen, Trung Hai Nguyen
, T. Ngoc Han Pham
, Nguyen Truong Huy
, Mai Van Bay
, Minh Quan Pham
, Pham Cam Nam
, Van V. Vu
, Son Tung Ngo
:
Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. 204-211 - Rabindranath Paul
, Sandip Paul
:
Computational Study of Encapsulation of Polyaromatic Hydrocarbons by Endo-Functionalized Receptors in Nonpolar Medium. 212-225 - Pharit Kamsri
, Chayanin Hanwarinroj, Naruedon Phusi
, Thimpika Pornprom, Kampanart Chayajarus, Auradee Punkvang
, Nitima Suttipanta, Potjanee Srimanote, Khomson Suttisintong
, Chomphunuch Songsiriritthigul, Patchreenart Saparpakorn, Supa Hannongbua, Siriluk Rattanabunyong, Supaporn Seetaha
, Kiattawee Choowongkomon, Sanya Sureram, Prasat Kittakoop
, Poonpilas Hongmanee, Pitak Santanirand
, Zhaoqiang Chen, Weiliang Zhu
, Rosemary A. Blood, Yuiko Takebayashi
, Philip Hinchliffe
, Adrian J. Mulholland
, James Spencer
, Pornpan Pungpo
:
Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography. 226-234 - Wenli Wang, Lan Zheng, Wei Li, Chen Zhu, Weiqing Peng, Bing Han, Wei Fu
:
Design, Synthesis, and Structure-Activity Relationship Studies of Novel Indolyalkylpiperazine Derivatives as Selective 5-HT1A Receptor Agonists. 235-248 - Alex Zhou, Michael Schauperl
, Paul S. Nerenberg
:
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models. 249-258 - Mark A. J. Koenis, Olivier Visser, Lucas Visscher
, Wybren J. Buma
, Valentin P. Nicu
:
GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra. 259-267 - Miguel Ponce-Vargas
, Corentin Lefebvre
, Jean-Charles Boisson, Eric Henon
:
Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host-Guest Assemblies. 268-278 - Matthias Diem
, Chris Oostenbrink
:
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. 279-288 - Joseph M. Jakubowski, Asuka A. Orr
, Doan A. Le, Phanourios Tamamis
:
Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. 289-305 - Zhenlu Li
, Matthias Buck:
Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface. 306-315 - Quan Van Vo
, Adam Mechler
:
In Silico Study of the Radical Scavenging Activities of Natural Indole-3-Carbinols. 316-321 - Leandro Oliveira Bortot
, Zahedeh Bashardanesh, David van der Spoel
:
Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. 322-331 - Maninder Singh
, Vikash Kumar
, Kamakshi Sikka, Ravi Thakur
, Munesh Kumar Harioudh, Durga Prasad Mishra, Jimut Kanti Ghosh, Mohammad Imran Siddiqi
:
Computational Design of Biologically Active Anticancer Peptides and Their Interactions with Heterogeneous POPC/POPS Lipid Membranes. 332-341 - Abdennour Braka, Norbert Garnier
, Pascal Bonnet
, Samia Aci-Sèche:
Residence Time Prediction of Type 1 and 2 Kinase Inhibitors from Unbinding Simulations. 342-348 - Maywan Hariono
, Rina F. Nuwarda
, Muhammad Yusuf
, Rollando Rollando
, Riris Istighfari Jenie, Belal Al-Najjar
, Jeffry Julianus, Kevin C. Putra, Ervan S. Nugroho, Yohanes K. Wisnumurti, Sangga P. Dewa, Benedictus W. Jati, Reynaldo Tiara, Ratna D. Ramadani, Lailatul Qodria, Habibah A. Wahab
:
Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling. 349-359 - Eva-Maria Zangerl-Plessl
, Martin Berger
, Martina Drescher, Yong Chen, Wei Wu, Nuno Maulide
, Michael Sanguinetti, Anna Stary-Weinzinger
:
Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574. 360-371 - Luca Pinzi
, Giulio Rastelli
:
Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank. 372-390 - Sheng Chen
, Zhe Sun, Lihua Lin, Zifeng Liu, Xun Liu, Yutian Chong, Yutong Lu, Huiying Zhao
, Yuedong Yang
:
To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. 391-399 - Cong Fan
, Ping-pui Wong
, Huiying Zhao
:
DStruBTarget: Integrating Binding Affinity with Structure Similarity for Ligand-Binding Protein Prediction. 400-409 - Xiaoqiang Huang
, Robin Pearce, Yang Zhang
:
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. 410-420 - Neeraj Kumar
, Damini Sood
, Neera Sharma, Ramesh Chandra
:
Multiepitope Subunit Vaccine to Evoke Immune Response against Acute Encephalitis. 421-433
Volume 60, Number 2, February 2020
- Thereza A. Soares
, Habibah A. Wahab
:
Outlook on the Development and Application of Molecular Simulations in Latin America. 435-438 - Lucas A. Silva
, Julio C. G. Correia
:
GEMS-Pack: A Graphical User Interface for the Packmol Program. 439-443 - Roy González-Alemán
, David Hernández-Castillo
, Alejandro Rodríguez-Serradet
, Julio Caballero
, Erix Wiliam Hernández-Rodríguez
, Luis Alberto Montero-Cabrera
:
BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations. 444-448 - Ariane Nunes-Alves
:
From Brazil to Germany: Challenges and Advantages. 449-451 - Gabriel Ravanhani Schleder
, Antonio Claudio M. Padilha
, Alexandre Reily Rocha
, Gustavo Martini Dalpian
, Adalberto Fazzio
:
Ab Initio Simulations and Materials Chemistry in the Age of Big Data. 452-459 - Ariel Fernández
:
Artificial Intelligence Steering Molecular Therapy in the Absence of Information on Target Structure and Regulation. 460-466 - Roy González-Alemán
, David Hernández-Castillo
, Julio Caballero
, Luis Alberto Montero-Cabrera
:
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution. 467-472 - Denys E. S. Santos
, Frederico J. S. Pontes, Roberto D. Lins
, Kaline Coutinho
, Thereza A. Soares
:
SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. 473-484 - Rafael Maglia de Souza
, Leonardo José Amaral de Siqueira
, Mikko Karttunen
, Luis Gustavo Dias
:
Molecular Dynamics Simulations of Polymer-Ionic Liquid (1-Ethyl-3-methylimidazolium Tetracyanoborate) Ternary Electrolyte for Sodium and Potassium Ion Batteries. 485-499 - Eduardo R. Almeida
, Leonardo A. De Souza
, Wagner B. De Almeida
, Hélio F. Dos Santos
:
Chemically Modified Carbon Nanohorns as Nanovectors of the Cisplatin Drug: A Molecular Dynamics Study. 500-512 - Edvonaldo Florêncio e Silva, Edna S. Machado, Iane B. Vasconcelos, Severino A. Junior
, José Diogo L. Dutra, Ricardo Oliveira Freire
, Nivan B. da Costa Jr.:
Are the Absorption Spectra of Doxorubicin Properly Described by Considering Different Tautomers? 513-521 - Rafael Maglia de Souza
, R. H. Ratochinski, Mikko Karttunen
, Luis Gustavo Dias
:
Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles. 522-536 - Krys E. A. Batista
, Vivianne K. Ocampo-Restrepo, Marinalva D. Soares, Marcos G. Quiles
, Maurício J. Piotrowski
, Juarez L. F. Da Silva
:
Ab Initio Investigation of CO2 Adsorption on 13-Atom 4d Clusters. 537-545 - Paulo Henrique Borges Ferreira
, Frederico Campos Freitas
, Michelle E. McCully
, Gabriel Gouvêa Slade, Ronaldo Junio de Oliveira
:
The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. 546-561 - Felipe R. S. Santos
, William G. Lima
, Eduardo H. B. Maia, Letícia C. Assis, Danilo Davyt, Alex Gutterres Taranto, Jaqueline M. S. Ferreira
:
Identification of a Potential Zika Virus Inhibitor Targeting NS5 Methyltransferase Using Virtual Screening and Molecular Dynamics Simulations. 562-568 - Franccesca Fornasier
, Lucas Miguel Pereira Souza
, Felipe Rodrigues Souza
, Franceline Reynaud
, André Silva Pimentel
:
Lipophilicity of Coarse-Grained Cholesterol Models. 569-577 - Igor Barden Grillo, Gabriel Aires Urquiza-Carvalho
, José Fernando Ruggiero Bachega, Gerd Bruno Rocha
:
Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors. 578-591 - Fiorella Cravero
, Santiago Schustik, María Jimena Martínez, Gustavo E. Vazquez
, Mónica Fátima Díaz
, Ignacio Ponzoni
:
Feature Selection for Polymer Informatics: Evaluating Scalability and Robustness of the FS4RVDD Algorithm Using Synthetic Polydisperse Data Sets. 592-603 - Laura Mortara, Hernan Chaimovich
, Iolanda M. Cuccovia, Dominik Horinek
, Filipe S. Lima
:
Dehydration Determines Hydrotropic Ion Affinity for Zwitterionic Micelles. 604-610 - Fernando Alvarez-Ramírez
, Yosadara Ruiz-Morales
:
Database of Nuclear Independent Chemical Shifts (NICS) versus NICSZZ of Polycyclic Aromatic Hydrocarbons (PAHs). 611-620 - Lucas G. Viviani
, Erika Piccirillo
, Henning Ulrich
, Antonia T. do Amaral
:
Virtual Screening Approach for the Identification of Hydroxamic Acids as Novel Human Ecto-5′-Nucleotidase Inhibitors. 621-630 - Pablo R. Arantes
, Conrado Pedebos, Marcelo Depólo Polêto
, Laercio Pol-Fachin, Hugo Verli
:
The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains. 631-643 - Yaicel G. Proenza
, Ricardo L. Longo:
Simulation of the Adsorption and Release of Large Drugs by ZIF-8. 644-652 - Murilo H. Teixeira
, Felipe Curtolo
, Sofia R. G. Camilo, Martin J. Field
, Peng Zheng
, Hongbin Li
, Guilherme Menegon Arantes
:
Modeling the Hydrolysis of Iron-Sulfur Clusters. 653-660 - Jessé G. Neumann, Hubert Stassen
:
Anion Effect on Gas Absorption in Imidazolium-Based Ionic Liquids. 661-666 - Karina B. Santos
, Isabella A. Guedes
, Ana L. M. Karl
, Laurent Emmanuel Dardenne
:
Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein-Peptide Data Set. 667-683 - João L. de Meirelles, Felipe C. Nepomuceno, Jorge Peña-García, Ricardo Rodríguez-Schmidt, Horacio Pérez Sánchez
, Hugo Verli
:
Current Status of Carbohydrates Information in the Protein Data Bank. 684-699 - Sarah Arvelos
, Carla Eponina Hori
:
ReaxFF Study of Ethanol Oxidation in O2/N2 and O2/CO2 Environments at High Temperatures. 700-713 - Caio P. de Castro, Thiago A. de Assis
, Roberto Rivelino
, Fernando de B. Mota, Caio M. C. de Castilho, Richard G. Forbes:
Modeling the Field Emission Enhancement Factor for Capped Carbon Nanotubes Using the Induced Electron Density. 714-721 - Juan I. Melo
, Alejandro F. Maldonado, Gustavo A. Aucar
:
Performance of the LRESC Model on top of DFT Functionals for Relativistic NMR Shielding Calculations. 722-730 - Felipe R. S. Santos
, Damiana A. F. Nunes, William G. Lima
, Danilo Davyt, Luciana L. Santos
, Alex G. Taranto, Jaqueline M. S. Ferreira
:
Identification of Zika Virus NS2B-NS3 Protease Inhibitors by Structure-Based Virtual Screening and Drug Repurposing Approaches. 731-737 - Paulo R. M. Pereira, Jéssica de O. Araújo
, José Rogério A. Silva
, Cláudio Nahum Alves
, Jerônimo Lameira
, Anderson Henrique Lima e Lima
:
Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. 738-746 - Alvaro J. Lopez
, Emília P. Barros, Leandro Martínez
:
On the Interpretation of subtilisin Carlsberg Time-Resolved Fluorescence Anisotropy Decays: Modeling with Classical Simulations. 747-755 - Giacomo Rossino
, Ivana Orellana, Julio Caballero
, Dirk Schepmann, Bernhard Wünsch
, Marta Rui, Daniela Rossi
, Mariela González-Avendaño, Simona Collina
, Ariela Vergara Jaque
:
New Insights into the Opening of the Occluded Ligand-Binding Pocket of Sigma1 Receptor: Binding of a Novel Bivalent RC-33 Derivative. 756-765 - Jorddy Neves Cruz
, Mozaniel Santana de Oliveira, Sebastião Gomes Silva
, Antonio Pedro da Silva Souza Filho, Daniel Santiago Pereira
, Anderson Henrique Lima e Lima
, Eloisa Helena de Aguiar Andrade
:
Insight into the Interaction Mechanism of Nicotine, NNK, and NNN with Cytochrome P450 2A13 Based on Molecular Dynamics Simulation. 766-776 - Rodrigo Aguayo-Ortiz
, Laura Dominguez
:
Effects of Mutating Trp42 Residue on γD-Crystallin Stability. 777-785 - Brianda L. Santini, Matías Zúñiga-Bustos
, Abraham Vidal-Limon
, Joel B. Alderete
, Sergio A. Aguila
, Verónica A. Jiménez
:
In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy. 786-793 - N. R. Carina Alves
, Adali Pecci, Lautaro D. Alvarez
:
Structural Insights into the Ligand Binding Domain of the Glucocorticoid Receptor: A Molecular Dynamics Study. 794-804 - Antistio Alviz-Amador
, Rodrigo Galindo-Murillo
, Humberto Pérez-González
, Erika Rodríguez-Cavallo
, Ricardo Vivas-Reyes
, Darío Méndez-Cuadro
:
Effect of 4-HNE Modification on ZU5-ANK Domain and the Formation of Their Complex with β-Spectrin: A Molecular Dynamics Simulation Study. 805-820 - Elias D. López
, Osvaldo Burastero
, Juan Pablo Arcon
, Lucas A. Defelipe
, Natalie G. Ahn, Marcelo A. Marti
, Adrian Gustavo Turjanski
:
Kinase Activation by Small Conformational Changes. 821-832 - Federico A. Olivieri
, Osvaldo Burastero
, Salvador I. Drusin
, Lucas A. Defelipe
, Diana E. Wetzler
, Adrian Gustavo Turjanski, Marcelo A. Marti
:
Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations. 833-842 - Jonathan Alexis Semelak
, Federica Battistini
, Rafael Radi
, Madia Trujillo
, Ari Zeida
, Dario A. Estrin
:
Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. 843-853 - Cecilia Prudkin-Silva
, Oscar E. Pérez
, Karina D. Martínez
, Fernando Luís Barroso da Silva
:
Combined Experimental and Molecular Simulation Study of Insulin-Chitosan Complexation Driven by Electrostatic Interactions. 854-865 - Ángel Santiago
, Rodrigo Said Razo-Hernández
, Nina Pastor
:
Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. 866-879 - Clauber Henrique Costa
, Vinícius Bonatto
, Alberto M. dos Santos, Jerônimo Lameira
, Andrei Leitão
, Carlos Alberto Montanari
:
Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors. 880-889 - André A. O. Reis, Raphael S. R. Sayegh, Sandro R. Marana
, Guilherme Menegon Arantes
:
Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation-π Contacts in Proteins. 890-897 - Jocelyn Solorza, Rodrigo Recabarren, Jans H. Alzate-Morales
:
Molecular Insights into the Trapping Effect of Ca2+ in Protein Kinase A: A Molecular Dynamics Study. 898-914 - Fernanda Mendoza
, Fabiola E. Medina
, Verónica A. Jiménez
, Gonzalo A. Jaña
:
Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study. 915-922 - Vanesa Racigh, Agustín Ormazábal
, Juliana Palma
, Gustavo Pierdominici-Sottile
:
Positively Charged Residues in the Head Domain of P2X4 Receptors Assist the Binding of ATP. 923-932 - Fernanda Mendoza
, Gonzalo A. Jaña
:
Unveiling the Dynamical and Structural Features That Determine the Orientation of the Acceptor Substrate in the Landomycin Glycosyltransferase LanGT2 and Its Variant with C-Glycosylation Activity. 933-943 - Sergio A. Poveda-Cuevas
, Catherine Etchebest
, Fernando Luís Barroso da Silva
:
Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. 944-963 - Pablo G. Garay
, Exequiel E. Barrera, Sergio Pantano
:
Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. 964-973 - Matías Martínez, Christopher D. Cooper
, Adolfo B. Poma
, Horacio V. Guzman
:
Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. 974-981 - Fernando Bruno da Silva
, Vinícius Martins de Oliveira
, Murilo Nogueira Sanches
, Vinícius G. Contessoto
, Vitor B. P. Leite
:
Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. 982-988 - Simón Poblete
, Tomás Pérez-Acle
:
Brief Comparison between Experimental and Computationally Generated Ensembles of RNA Dinucleotides. 989-994 - Pilar A. Vásquez, Felipe Vidal, Josefa Torres, Verónica A. Jiménez
, Leonardo Guzmán
:
Rational Design and In Vitro Evaluation of Novel Peptides Binding to Neuroligin-1 for Synaptic Targeting. 995-1004 - José X. Lima Neto
, Katyanna S. Bezerra, Emmanuel D. Barbosa
, Jonas I. N. Oliveira, Vinícius Manzoni
, Vanessa P. Soares-Rachetti, Eudenílson L. Albuquerque, Umberto Laino Fulco
:
Exploring the Binding Mechanism of GABAB Receptor Agonists and Antagonists through in Silico Simulations. 1005-1018 - Natali Acosta-Tapia
, Johan Fabian Galindo
, Rosa Baldiris:
Insights into the Effect of Lowe Syndrome-Causing Mutation p.Asn591Lys of OCRL-1 through Protein-Protein Interaction Networks and Molecular Dynamics Simulations. 1019-1027 - Mariana Laureano de Souza, Celso de Oliveira Rezende Junior
, Rafaela Salgado Ferreira
, Rocio Marisol Espinoza Chávez
, Leonardo L. G. Ferreira, Brian W. Slafer, Luma G. Magalhães, Renata Krogh, Glaucius Oliva
, Fabio Cardoso Cruz, Luiz Carlos Dias, Adriano D. Andricopulo
:
Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach. 1028-1041 - Ernesto Contreras-Torres
, Yovani Marrero-Ponce
, Julio E. Terán
, César R. García-Jacas
, Carlos A. Brizuela, Juan Carlos Sánchez-Rodríguez:
MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. 1042-1059 - Marcelo Querino Lima Afonso
, Néli José da Fonseca Jr., Lucas Carrijo de Oliveira
, Francisco Pereira Lobo
, Lucas Bleicher
:
Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family. 1060-1068
Volume 60, Number 3, March 2020
- Igor V. Tetko, Alexander Tropsha:
Joint Virtual Special Issue on Computational Toxicology. 1069-1071 - Kenneth M. Merz Jr.
, Gianni De Fabritiis, Guo-Wei Wei:
JCIM Special Issue on Generative Models for Molecular Design. 1072 - Jingru Xie, Kexin Zhang, Aaron T. Frank
:
PyShifts: A PyMOL Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles. 1073-1078 - Jocelyn Sunseri
, David Ryan Koes
:
libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. 1079-1084 - Oya Wahl
, Thomas Sander:
Tautobase: An Open Tautomer Database. 1085-1089 - Devendra K. Dhaked
, Laura Guasch, Marc C. Nicklaus
:
Tautomer Database: A Comprehensive Resource for Tautomerism Analyses. 1090-1100 - Thanh-Hoang Nguyen-Vo
, Loc Nguyen, Nguyet Do, Thien-Ngan Nguyen, Khang Trinh, Hung Cao, Ly Le
:
Plant Metabolite Databases: From Herbal Medicines to Modern Drug Discovery. 1101-1110 - Ece Asilar
, Jennifer Hemmerich
, Gerhard F. Ecker
:
Image Based Liver Toxicity Prediction. 1111-1121 - Minyi Su
, Guoqin Feng, Zhihai Liu
, Yan Li
, Renxiao Wang
:
Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set? 1122-1136 - Gyoung S. Na, Hyun Woo Kim
, Hyunju Chang
:
Costless Performance Improvement in Machine Learning for Graph-Based Molecular Analysis. 1137-1145 - Na Le Dang
, Matthew K. Matlock
, Tyler B. Hughes
, S. Joshua Swamidass
:
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors. 1146-1164 - Shimin Su
, Yuyao Yang
, Hanlin Gan, Shuangjia Zheng
, Fenglong Gu, Chao Zhao, Jun Xu
:
Predicting the Feasibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reactions Using a Recurrent Neural Network with a Self-Attention Mechanism. 1165-1174 - Francesca Grisoni
, Michael Moret, Robin Lingwood, Gisbert Schneider
:
Bidirectional Molecule Generation with Recurrent Neural Networks. 1175-1183 - Yunqi Shao
, Matti Hellström
, Pavlin D. Mitev
, Lisanne Knijff, Chao Zhang
:
PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials. 1184-1193 - Edward Kim
, Zach Jensen
, Alexander van Grootel, Kevin Huang, Matthew Staib, Sheshera Mysore
, Haw-Shiuan Chang
, Emma Strubell, Andrew McCallum, Stefanie Jegelka, Elsa Olivetti
:
Inorganic Materials Synthesis Planning with Literature-Trained Neural Networks. 1194-1201 - Jie Xia
, Zhenyi Wang, Yi Huan, Wenjie Xue, Xing Wang, Yuxi Wang, Zhenming Liu
, Jui-Hua Hsieh
, Liangren Zhang, Song Wu, Zhufang Shen, Hongmin Zhang
, Xiang Simon Wang
:
Pose Filter-Based Ensemble Learning Enables Discovery of Orally Active, Nonsteroidal Farnesoid X Receptor Agonists. 1202-1214 - Cecile Valsecchi
, Francesca Grisoni
, Viviana Consonni
, Davide Ballabio
:
Consensus versus Individual QSARs in Classification: Comparison on a Large-Scale Case Study. 1215-1223 - G. C. Loh
, H.-C. Lee, X. Y. Tee, P. S. Chow
, Jianwei Zheng
:
Viscosity Prediction of Lubricants by a General Feed-Forward Neural Network. 1224-1234 - Jian Jiang, Rui Wang
, Menglun Wang, Kaifu Gao, Duc Duy Nguyen, Guo-Wei Wei
:
Boosting Tree-Assisted Multitask Deep Learning for Small Scientific Datasets. 1235-1244 - Yifei Qi
, John Z. H. Zhang
:
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet. 1245-1252 - Devendra K. Dhaked
, Wolf-Dietrich Ihlenfeldt
, Hitesh Patel
, Victorien Delannée
, Marc C. Nicklaus
:
Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. 1253-1275 - Philip V. Toukach
, Ksenia S. Egorova
:
New Features of Carbohydrate Structure Database Notation (CSDB Linear), As Compared to Other Carbohydrate Notations. 1276-1289 - Joshua Kammeraad
, Jack Goetz, Eric Walker
, Ambuj Tewari, Paul M. Zimmerman
:
What Does the Machine Learn? Knowledge Representations of Chemical Reactivity. 1290-1301 - Oleksandr Kravchenko
, Anastasiia Varava, Florian T. Pokorny
, Didier Devaurs
, Lydia E. Kavraki
, Danica Kragic
:
A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction. 1302-1316 - Enrico Margiotta
, Stephanie C. C. van der Lubbe
, Lucas de Azevedo Santos
, Gábor Paragi, Stefano Moro
, Friedrich Matthias Bickelhaupt
, Célia Fonseca Guerra
:
Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. 1317-1328 - Duy Quang Dao
, Thi Thu Trang Phan, Thi Le Anh Nguyen
, Phan Thi Hoai Trinh, Thi Thanh Van Tran, Jong Seok Lee, Hee Jae Shin
, Byeoung-Kyu Choi:
Insight into Antioxidant and Photoprotective Properties of Natural Compounds from Marine Fungus. 1329-1351 - Maria Cecilia Barrera
, Miguel Jorge
:
A Polarization-Consistent Model for Alcohols to Predict Solvation Free Energies. 1352-1367 - Sébastien Dilly
, Mélanie Garnier, Marion Solé, Rémi Bailly, Nada Taib, Isabelle Bestel:
In Silico Identification of a Key Residue for Substrate Recognition of the Riboflavin Membrane Transporter RFVT3. 1368-1375 - Hideaki Takahashi
, Shun Sakuraba
, Akihiro Morita
:
Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform. 1376-1389 - Lorenzo Di Rienzo
, Edoardo Milanetti
, Josephine Alba
, Marco D'Abramo
:
Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors. 1390-1398 - Huynh Minh Hung
, Minh Tho Nguyen
, Phuong-Thao Tran
, Vi Khanh Truong
, James Chapman
, Le Huu Quynh Anh, Philippe Derreumaux
, Van V. Vu
, Son Tung Ngo
:
Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide. 1399-1408 - Tobias Hüfner-Wulsdorf
, Gerhard Klebe
:
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals. 1409-1423 - Shi Li, Balaji Sesha Sarath Pokuri
, Sean M. Ryno
, Asare Nkansah, Camron De'vine, Baskar Ganapathysubramanian, Chad M. Risko
:
Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach. 1424-1431 - Daniel Cappel
, Steven Jerome, Gerhard Hessler, Hans Matter:
Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. 1432-1444 - Jacinto Sandoval-Lira, Gustavo Mondragón-Solórzano
, Leonardo I. Lugo-Fuentes, Joaquín Barroso-Flores
:
Accurate Estimation of pKb Values for Amino Groups from Surface Electrostatic Potential (VS, min) Calculations: The Isoelectric Points of Amino Acids as a Case Study. 1445-1452 - Kristian Kríz
, Jan Rezác
:
Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design. 1453-1460 - Julian Zachmann, Eftichia Kritsi
, Anthi Tapeinou, Panagiotis Zoumpoulakis
, Theodore V. Tselios
, Minos-Timotheos Matsoukas
:
Combined Computational and Structural Approach into Understanding the Role of Peptide Binding and Activation of Melanocortin Receptor 4. 1461-1468 - Silvia Rinaldi
, Giorgio Colombo
, Antonella Paladino
:
Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute. 1469-1480 - Laura Pedraza-González
, María Del Carmen Marín
, Alejandro N. Jorge
, Tyler D. Ruck
, Xuchun Yang
, Alessio Valentini
, Massimo Olivucci
, Luca De Vico
:
Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins. 1481-1493 - Joseph Katigbak, Haotian Li, David Rooklin, Yingkai Zhang
:
AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. 1494-1508 - Jonathan Fine, Janez Konc
, Ram Samudrala, Gaurav Chopra
:
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. 1509-1527 - Lucia Fusani, David S. Palmer
, Don O. Somers, Ian D. Wall:
Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. 1528-1539 - Yue Chen, Junhao Li, Zengrui Wu, Guixia Liu
, Honglin Li
, Yun Tang
, Weihua Li
:
Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. 1540-1550 - Rongfeng Zou
, Yang Zhou
, Yong Wang
, Guanglin Kuang
, Hans Ågren
, Junchen Wu
, Yaoquan Tu
:
Free Energy Profile and Kinetics of Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2. 1551-1558 - Vladimír Sládek
, Ryuhei Harada
, Yasuteru Shigeta
:
Protein Dynamics and the Folding Degree. 1559-1567 - Christina Nutschel, Alexander Fulton, Olav Zimmermann, Ulrich Schwaneberg
, Karl-Erich Jaeger
, Holger Gohlke
:
Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. 1568-1584 - Lijuan Yan, Yongjun Liu
:
The Retaining Mechanism of Xylose Transfer Catalyzed by Xyloside α-1, 3-Xylosyltransferase (XXYLT1): a Quantum Mechanics/Molecular Mechanics Study. 1585-1594 - Maciej Pyrka, Maciej Maciejczyk
:
Why Purine Nucleoside Phosphorylase Ribosylates 2, 6-Diamino-8-azapurine in Noncanonical Positions? A Molecular Modeling Study. 1595-1606 - Xiaozheng Zhang
, Yibo Wang
, Hongshuang Wang, Hongyuan Li, Tianshu Zhang, Yinghua Peng, Xiaohui Wang
:
Exploring Methamphetamine Nonenantioselectively Targeting Toll-like Receptor 4/Myeloid Differentiation Protein 2 by in Silico Simulations and Wet-Lab Techniques. 1607-1613 - Lindy Astl, Gennady M. Verkhivker
:
Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks. 1614-1631 - Guillem Vila-Julià
, José M. Granadino-Roldán
, Juan Jesús Pérez
, Jaime Rubio-Martinez
:
Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides. 1632-1643 - Maciej Majewski
, Xavier Barril
:
Structural Stability Predicts the Binding Mode of Protein-Ligand Complexes. 1644-1651 - Hristina R. Zhekova
, Toshie Sakuma, Ryan Johnson, Susanna C. Concilio, Patrycja J. Lech, Igor Zdravkovic, Mirna Damergi, Lukkana Suksanpaisan, Kah-Whye Peng, Stephen J. Russell
, Sergei Yu Noskov
:
Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). 1652-1665 - José Rogério A. Silva
, Lorenzo Cianni
, Deborah Araujo, Pedro Henrique Jatai Batista
, Daniela de Vita
, Fabiana Rosini, Andrei Leitão
, Jerônimo Lameira
, Carlos Alberto Montanari
:
Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism. 1666-1677 - Dinesh Kumar Sriramulu
, Sun-Gu Lee
:
Combinatorial Effect of Ligand and Ligand-Binding Site Hydrophobicities on Binding Affinity. 1678-1684 - Jui-Hung Yuan, Sungho Bosco Han, Stefan Richter, Rebecca C. Wade
, Daria B. Kokh
:
Druggability Assessment in TRAPP Using Machine Learning Approaches. 1685-1699 - Chaoqun Li
, Xiaojia Zhao, Wei Liu
, Fangqian Yin, Junping Hu, Guangjie Zhang, Guangju Chen:
DNA Structural Distortions Induced by a Monofunctional Trinuclear Platinum Complex with Various Cross-Links Using Molecular Dynamics Simulation. 1700-1708 - Satoshi Yasuda, Tomoki Akiyama, Sayaka Nemoto, Tomohiko Hayashi, Tetsuya Ueta, Keiichi Kojima
, Takashi Tsukamoto
, Satoru Nagatoishi
, Kouhei Tsumoto
, Yuki Sudo
, Masahiro Kinoshita
, Takeshi Murata
:
Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained. 1709-1716 - Liang Dai
, Zhiqi Feng
, Rili Zha
, Keguang Cheng, Xiaoan Wen
, Hongbin Sun
, Haoliang Yuan
:
Discovery of Novel Peroxisome Proliferator-Activated Receptor α (PPARα) Agonists by Virtual Screening and Biological Evaluation. 1717-1727 - Carles Perez
, Daniel Soler
, Robert Soliva
, Victor Guallar
:
FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design. 1728-1736 - Abdurrahman Olgaç
, Andrea Carotti
, Christian Kretzer, Stephanie Zergiebel, Andreas Seeling, Ulrike Garscha
, Oliver Werz
, Antonio Macchiarulo, Erden Banoglu
:
Discovery of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by Exploiting a Multistep Virtual Screening Protocol. 1737-1748 - Holli-Joi Sullivan
, Amanda Tursi, Kelly Moore, Alexandra Campbell, Cecilia Floyd, Chun Wu
:
Binding Interactions of Ergotamine and Dihydroergotamine to 5-Hydroxytryptamine Receptor 1B (5-HT1b) Using Molecular Dynamics Simulations and Dynamic Network Analysis. 1749-1765 - Ferah Comert Onder
, Serdar Durdagi
, Kader Sahin
, Bulent Ozpolat
, Mehmet Ay
:
Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors. 1766-1778 - Julio Gomis-Tena
, Brandon M. Brown, Jordi Cano
, Beatriz Trénor, Pei-Chi Yang, Javier Saiz, Colleen E. Clancy, Lucía Romero
:
When Does the IC50 Accurately Assess the Blocking Potency of a Drug? 1779-1790 - Nasim Ahmadian, Faramarz Mehrnejad
, Mehriar Amininasab:
Molecular Insight into the Interaction between Camptothecin and Acyclic Cucurbit[4]urils as Efficient Nanocontainers in Comparison with Cucurbit[7]uril: Molecular Docking and Molecular Dynamics Simulation. 1791-1803 - Giuseppe Deganutti
, Stefano Moro
, Christopher A. Reynolds
:
A Supervised Molecular Dynamics Approach to Unbiased Ligand-Protein Unbinding. 1804-1817 - Tobias Hüfner-Wulsdorf
, Gerhard Klebe
:
Role of Water Molecules in Protein-Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics. 1818-1832 - Naoki Watanabe, Masahiro Murata, Teppei Ogawa, Christopher J. Vavricka
, Akihiko Kondo
, Chiaki Ogino
, Michihiro Araki
:
Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions. 1833-1843 - Agnieszka S. Karczynska
, Karolina Zieba, Urszula Uciechowska, Magdalena A. Mozolewska, Pawel Krupa
, Emilia A. Lubecka, Agnieszka G. Lipska, Celina Sikorska
, Sergey A. Samsonov
, Adam K. Sieradzan
, Artur Gieldon
, Adam Liwo
, Rafal Slusarz
, Magdalena Slusarz
, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
:
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. 1844-1864 - Jiansheng Wu
, Yi Sun, Wallace K. B. Chan
, Yanxiang Zhu
, Wenyong Zhu, Wanqing Huang, Haifeng Hu, Shancheng Yan, Tao Pang, Xiaoyan Ke, Fei Li:
Homologous G Protein-Coupled Receptors Boost the Modeling and Interpretation of Bioactivities of Ligand Molecules. 1865-1875 - Zongyu Wang, Wenying He, Jijun Tang, Fei Guo:
Identification of Highest-Affinity Binding Sites of Yeast Transcription Factor Families. 1876-1883 - Mattia Miotto
, Lorenzo Di Rienzo
, Pietro Corsi, Giancarlo Ruocco
, Domenico Raimondo
, Edoardo Milanetti
:
Simulated Epidemics in 3D Protein Structures to Detect Functional Properties. 1884-1891 - Ayisha Zia
, Muhammad Imran, Sajid Rashid:
In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity. 1892-1909 - Robert P. Sheridan
, Min Wang, Andy Liaw, Junshi Ma, Eric M. Gifford:
Correction to Extreme Gradient Boosting as a Method for Quantitative Structure-Activity Relationships. 1910
Volume 60, Number 4, April 2020
- Peter R. Curran
, Chris J. Radoux, Mihaela D. Smilova, Richard A. Sykes, Alicia P. Higueruelo
, Anthony R. Bradley, Brian D. Marsden, David R. Spring
, Tom L. Blundell, Andrew R. Leach
, William R. Pitt
, Jason C. Cole
:
Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design. 1911-1916 - Miroslav Suruzhon
, Tharindu Senapathi
, Michael S. Bodnarchuk
, Russell C. Viner, Ian D. Wall, Christopher B. Barnett, Kevin J. Naidoo
, Jonathan W. Essex
:
ProtoCaller: Robust Automation of Binding Free Energy Calculations. 1917-1921 - Gudrun Gygli
, Jürgen Pleiss:
Simulation Foundry: Automated and F.A.I.R. Molecular Modeling. 1922-1927 - Balaranjan Selvaratnam
, Ranjit T. Koodali
, Pere Miró
:
Application of Symmetry Functions to Large Chemical Spaces Using a Convolutional Neural Network. 1928-1935 - James Houston, Frank G. Glavin
, Michael G. Madden:
Robust Classification of High-Dimensional Spectroscopy Data Using Deep Learning and Data Synthesis. 1936-1954 - Amanda J. Minnich
, Kevin McLoughlin
, Margaret Tse, Jason Deng, Andrew Weber, Neha Murad, Benjamin D. Madej, Bharath Ramsundar, Tom Rush, Stacie Calad-Thomson, Jim Brase, Jonathan E. Allen
:
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery. 1955-1968 - Robert P. Sheridan
, Prabha Karnachi, Matthew Tudor
, Yuting Xu
, Andy Liaw, Falgun Shah, Alan C. Cheng
, Elizabeth Joshi
, Meir Glick, Juan Alvarez:
Experimental Error, Kurtosis, Activity Cliffs, and Methodology: What Limits the Predictivity of Quantitative Structure-Activity Relationship Models? 1969-1982 - Fergus Imrie
, Anthony R. Bradley, Mihaela van der Schaar, Charlotte M. Deane
:
Deep Generative Models for 3D Linker Design. 1983-1995 - Juhwan Noh, Geun Ho Gu
, Sungwon Kim, Yousung Jung
:
Uncertainty-Quantified Hybrid Machine Learning/Density Functional Theory High Throughput Screening Method for Crystals. 1996-2003 - Hong Wang, Yunchao Xie
, Dawei Li, Heng Deng, Yunxin Zhao, Ming Xin, Jian Lin
:
Rapid Identification of X-ray Diffraction Patterns Based on Very Limited Data by Interpretable Convolutional Neural Networks. 2004-2011 - Valentin Goussard, François Duprat, Jean-Luc Ploix, Gérard Dreyfus
, Véronique Nardello-Rataj
, Jean-Marie Aubry:
A New Machine-Learning Tool for Fast Estimation of Liquid Viscosity. Application to Cosmetic Oils. 2012-2023 - Youngchun Kwon, Dongseon Lee, Youn-Suk Choi
, Myeonginn Kang, Seokho Kang
:
Neural Message Passing for NMR Chemical Shift Prediction. 2024-2030 - Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou
, Dong-Sheng Cao
:
Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. 2031-2043 - Shuzhe Wang
, Jagna Witek, Gregory A. Landrum
, Sereina Riniker
:
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. 2044-2058 - Edward J. Beard
, Jacqueline M. Cole
:
ChemSchematicResolver: A Toolkit to Decode 2D Chemical Diagrams with Labels and R-Groups into Annotated Chemical Named Entities. 2059-2072 - Hiroshi Nakano
, Tomoyuki Miyao
, Kimito Funatsu
:
Exploring Topological Pharmacophore Graphs for Scaffold Hopping. 2073-2081 - Tao Zeng
, Zhihong Liu
, Jingyuan Zhuang, Yitao Jiang, Wengan He, Hongjuan Diao, Nan Lv, Yongxing Jian, Danhong Liang, Yufan Qiu, Rong Zhang, Fan Zhang, Xiaowen Tang, Ruibo Wu
:
TeroKit: A Database-Driven Web Server for Terpenome Research. 2082-2090 - Michael J. Bower
, Alex M. Aronov, Thomas Cleveland, Niresh Hariparsad, Georgia B. McGaughey
, Daniel R. McMasters
, Xiaodan Zhang, Brian Goldman:
Smallest Maximum Intramolecular Distance: A Novel Method to Mitigate Pregnane Xenobiotic Receptor Activation. 2091-2099 - Jade Simões de Castro
, Caio Henrique Pinke Rodrigues
, Aline Thaís Bruni
:
In Silico Infrared Characterization of Synthetic Cannabinoids by Quantum Chemistry and Chemometrics. 2100-2114 - Juan José Gamboa-Carballo
, Anthuan Ferino-Pérez
, Vijay Kumar Rana
, Joëlle Levalois-Grützmacher
, Sarra Gaspard, Luis Alberto Montero-Cabrera
, Ulises Javier Jáuregui-Haza
:
Theoretical Evaluation of the Molecular Inclusion Process between Chlordecone and Cyclodextrins: A New Method for Mitigating the Basis Set Superposition Error in the Case of an Implicit Solvation Model. 2115-2125 - Stefan Seritan
, Keiran Thompson
, Todd J. Martínez
:
TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations. 2126-2137 - Erick López-Chávez, Gerardo Pérez-Hernández
, Felipe Aparicio
, Salomón de Jesús Alas
:
On the Thermal Stability of O6-Methylguanine-DNA Methyltransferase from Archaeon Pyrococcus kodakaraensis by Molecular Dynamics Simulations. 2138-2154 - Alexander St. John, Michael W. Roth, Lucyna Firlej
, Bogdan Kuchta
, Fabrice Charra
, Carlos Wexler
:
Self-Assembled Two-Dimensional Nanoporous Crystals as Molecular Sieves: Molecular Dynamics Studies of 1, 3, 5-Tristyrilbenzene-Cn Superstructures. 2155-2168 - Rohit Goswami
, Amrita Goswami
, Jayant K. Singh
:
d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations. 2169-2177 - Philipp S. Schmalhorst
, Andreas Bergner
:
A Grid Map Based Approach to Identify Nonobvious Ligand Design Opportunities in 3D Protein Structure Ensembles. 2178-2188 - Hugo Guterres
, Wonpil Im
:
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. 2189-2198 - Qiyuan Zhao
, Brett M. Savoie
:
Self-Consistent Component Increment Theory for Predicting Enthalpy of Formation. 2199-2207 - Zheng Wan, Guobing Zhou
, Zhongyang Dai, Li Li, Na Hu, Xiangshu Chen, Zhen Yang:
Separation Selectivity of CH4/CO2 Gas Mixtures in the ZIF-8 Membrane Explored by Dynamic Monte Carlo Simulations. 2208-2218 - Rao Huang
, Jian-Xiang Bi, Lei Li
, Yu-Hua Wen
:
Basin Hopping Genetic Algorithm for Global Optimization of PtCo Clusters. 2219-2228 - Arghya Chakravorty
, Shailesh Kumar Panday
, Swagata Pahari
, Shan Zhao, Emil Alexov
:
Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. 2229-2246 - Krzysztof K. Bojarski
, Agnieszka S. Karczynska, Sergey A. Samsonov
:
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study. 2247-2256 - Dong Song
, Hao Liu
, Ray Luo
, Hai-Feng Chen
:
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. 2257-2267 - Laust Moesgaard
, Peter Reinholdt
, Daniel Wüstner
, Jacob Kongsted
:
Modeling the Sterol-Binding Domain of Aster-A Provides Insight into Its Multiligand Specificity. 2268-2281 - Christopher Lockhart
, Amy K. Smith, Dmitri K. Klimov
:
Three Popular Force Fields Predict Consensus Mechanism of Amyloid β Peptide Binding to the Dimyristoylgylcerophosphocholine Bilayer. 2282-2293 - Linn S. M. Evenseth, Riccardo Ocello, Mari Gabrielsen
, Matteo Masetti
, Maurizio Recanatini
, Ingebrigt Sylte, Andrea Cavalli
:
Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. 2294-2303 - Johannes R. Loeffler
, Monica L. Fernández-Quintero, Michael Schauperl, Klaus R. Liedl
:
STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. 2304-2313 - Gerard Martínez-Rosell
, Silvia Lovera, Zara A. Sands, Gianni De Fabritiis
:
PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. 2314-2324 - Alena Randáková
, Dominik Nelic
, Vladimír Dolezal
, Esam E. El-Fakahany, John Boulos, Jan Jakubik
:
Agonist-Specific Conformations of the M2 Muscarinic Acetylcholine Receptor Assessed by Molecular Dynamics. 2325-2338 - Robert G. Brinson
, Luke W. Arbogast
, John P. Marino, Frank Delaglio
:
Best Practices in Utilization of 2D-NMR Spectral Data as the Input for Chemometric Analysis in Biopharmaceutical Applications. 2339-2355 - Martin Simonovsky, Joshua Meyers
:
DeeplyTough: Learning Structural Comparison of Protein Binding Sites. 2356-2366 - Hui Liu
, Wenhao Zhang
, Yinglong Song, Lei Deng, Shuigeng Zhou:
HNet-DNN: Inferring New Drug-Disease Associations with Deep Neural Network Based on Heterogeneous Network Features. 2367-2376 - Huanyu Tao, Yanjun Zhang, Sheng-You Huang
:
Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. 2377-2387 - Xuan Lv
, Jianwen Chen
, Yutong Lu, Zhiguang Chen, Nong Xiao, Yuedong Yang
:
Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. 2388-2395 - Sugunadevi Sakkiah, Carmine Leggett, Bohu Pan, Wenjing Guo
, Luis G. Valerio, Huixiao Hong
:
Development of a Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model. 2396-2404 - Panagiotis Lagarias, Kerry Barkan, Eva Tzortzini
, Margarita Stampelou, Eleni Vrontaki, Graham Ladds
, Antonios Kolocouris
:
Correction to 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. 2405-2406
Volume 60, Number 5, May 2020
- Giulia Palermo
, Yuji Sugita
, Willy Wriggers
, Rommie E. Amaro
:
Faces of Contemporary CryoEM Information and Modeling. 2407-2409 - James S. Fraser
, Kresten Lindorff-Larsen
, Massimiliano Bonomi
:
What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? 2410-2412 - Pilar Cossio
:
Need for Cross-Validation of Single Particle Cryo-EM. 2413-2418 - Mauricio G. S. Costa
, Charline Fagnen
, Catherine Vénien-Bryan
, David Perahia:
A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit). 2419-2423 - Caitlyn L. McCafferty, Eric J. Verbeke, Edward M. Marcotte
, David W. Taylor
:
Structural Biology in the Multi-Omics Era. 2424-2429 - Liam J. Worrall
, Jinhong Hu
, Natalie C. J. Strynadka
:
Aligning the Symmetry of the Type III Secretion System Needle Complex. 2430-2435 - Doo Nam Kim
, Dominik Gront
, Karissa Y. Sanbonmatsu
:
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. 2436-2442 - Luciano A. Abriata
, Matteo Dal Peraro
:
Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? 2443-2447 - Shirin Akbar, Sukanya Mozumder, Jayati Sengupta
:
Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. 2448-2457 - Michael A. Cianfrocco, Elizabeth H. Kellogg
:
What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. 2458-2469 - Thomas Dodd
, Chunli Yan, Ivaylo Ivanov
:
Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy. 2470-2483 - Suvrajit Maji
, Hstau Y. Liao, Ali Dashti, Ghoncheh Mashayekhi
, Abbas Ourmazd, Joachim Frank
:
Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding. 2484-2491 - Karim T. Mukaddem, Edward J. Beard, Batuhan Yildirim
, Jacqueline M. Cole
:
ImageDataExtractor: A Tool To Extract and Quantify Data from Microscopy Images. 2492-2509 - Jure Borisek
, Andrea Saltalamacchia, Angelo Spinello
, Alessandra Magistrato
:
Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators. 2510-2521 - Sumudu P. Leelananda, Steffen Lindert
:
Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. 2522-2532 - Marta Martínez
, A. Jiménez-Moreno, David Maluenda
, Erney Ramírez-Aportela
, Roberto Melero, Ana Cuervo
, Pablo Conesa
, Laura del Cano, Y. C. Fonseca, Rubén Sánchez García, David Strelák, J. J. Conesa, E. Fernández-Giménez, F. de Isidro
, Carlos Oscar Sánchez Sorzano, José María Carazo
, Roberto Marabini:
Integration of Cryo-EM Model Building Software in Scipion. 2533-2540 - Carlos F. Rodríguez
, Mohinder Pal, Hugo Muñoz-Hernandez
, Laurence H. Pearl, Oscar Llorca
:
Modeling of a 14 kDa RUVBL2-Binding Domain with Medium Resolution Cryo-EM Density. 2541-2551 - Agnel Praveen Joseph
, Ingvar C. Lagerstedt
, Arjen Jakobi
, Tom Burnley, Ardan Patwardhan
, Maya Topf, Martyn Winn:
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps. 2552-2560 - Andreas D. Schenk
, Simone Cavadini, Nicolas H. Thomä, Christel Genoud
:
Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE. 2561-2569 - Sandhya P. Tiwari
, Sahil Chhabra, Florence Tama
, Osamu Miyashita:
Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps. 2570-2580 - Evan Seitz
, Joachim Frank
:
POLARIS: Path of Least Action Analysis on Energy Landscapes. 2581-2590 - John W. Vant, Shae-Lynn J. Lahey, Kalyanashis Jana
, Mrinal Shekhar, Daipayan Sarkar
, Barbara H. Munk, Ulrich Kleinekathöfer
, Sumit Mittal
, Christopher N. Rowley
, Abhishek Singharoy
:
Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials. 2591-2604 - Yue Zhang
, R. Tammaro, Peter J. Peters
, R. B. G. Ravelli
:
Could Egg White Lysozyme be Solved by Single Particle Cryo-EM? 2605-2613 - Rui Xie, Yu-Xuan Chen
, Jia-Ming Cai, Yang Yang, Hong-Bin Shen
:
SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment. 2614-2625 - Julio A. Kovacs, Junha Song
, Manfred Auer, Jing He, Wade Hunter, Willy Wriggers
:
Correction of Missing-Wedge Artifacts in Filamentous Tomograms by Template-Based Constrained Deconvolution. 2626-2633 - Genki Terashi, Yuki Kagaya, Daisuke Kihara
:
MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. 2634-2643 - Salim Sazzed
, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He
:
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. 2644-2650
Volume 60, Number 6, June 2020
- Cynthia J. Burrows
, Shu Wang
, Hyun Jae Kim
, Gerald J. Meyer, Kirk Schanze
, T. Randall Lee, Jodie L. Lutkenhaus
, David Kaplan
, Christopher Jones
, Carolyn R. Bertozzi
, Laura Kiessling, Mary Beth Mulcahy, Craig Lindsley, M. G. Finn, Joel D. Blum, Prashant Kamat, Courtney Aldrich, Stuart Rowan, Bin Liu, Dennis Liotta, Paul S. Weiss, Deqing Zhang, Krishna N. Ganesh, Patrick M. Sexton, Harry A. Atwater, J. Justin Gooding, David T. Allen, Christopher A. Voigt, Jonathan V. Sweedler, Alanna Schepartz, Vincent Rotello, Sébastien Lecommandoux, Shana J. Sturla, Sharon Hammes-Schiffer, Jillian Buriak, Jonathan W. Steed, Hongwei Wu, Julie Zimmerman, Bryan Brooks, Phillip Savage, William Tolman, Thomas F. Hofmann, Joan F. Brennecke, Thomas A. Holme, Kenneth M. Merz Jr., Gustavo Scuseria, William Jorgensen, Gunda I. Georg, Shaomeng Wang, Philip Proteau, John R. Yates, Peter Stang, Gilbert C. Walker, Marc Hillmyer, Lynne S. Taylor, Teri W. Odom, Erick Carreira, Kai Rossen, Paul Chirik, Scott J. Miller, Anne McCoy, Joan-Emma Shea, Martin Zanni, Catherine Murphy, Gregory Scholes, Joseph A. Loo:
Update to Our Reader, Reviewer, and Author Communities - April 2020. 2651-2652 - Rommie E. Amaro
, Adrian J. Mulholland
:
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. 2653-2656 - Alex Zhavoronkov
:
Medicinal Chemists versus Machines Challenge: What Will It Take to Adopt and Advance Artificial Intelligence for Drug Discovery? 2657-2659 - Gabriela Falcón-Cano
, Christophe Molina
, Miguel Ángel Cabrera-Pérez
:
ADME Prediction with KNIME: Development and Validation of a Publicly Available Workflow for the Prediction of Human Oral Bioavailability. 2660-2667 - Federico Lazzari
, Andrea Salvadori, Giordano Mancini
, Vincenzo Barone
:
Molecular Perception for Visualization and Computation: The Proxima Library. 2668-2672 - Alejandro Varela-Rial
, Maciej Majewski
, Alberto Cuzzolin, Gerard Martínez-Rosell
, Gianni De Fabritiis
:
SkeleDock: A Web Application for Scaffold Docking in PlayMolecule. 2673-2677 - Remco Hens, Ahmadreza Rahbari
, Sebastián Caro-Ortiz
, Noura Dawass, Máté Erdos, Ali Poursaeidesfahani
, Hirad S. Salehi
, Alper T. Celebi, Mahinder Ramdin
, Othonas A. Moultos
, David Dubbeldam
, Thijs J. H. Vlugt
:
Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method. 2678-2682 - Zhengdan Zhu
, Zhijian Xu
, Weiliang Zhu
:
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. 2683-2696 - Gabriele Scalia
, Colin A. Grambow
, Barbara Pernici
, Yi-Pei Li
, William H. Green Jr.
:
Evaluating Scalable Uncertainty Estimation Methods for Deep Learning-Based Molecular Property Prediction. 2697-2717 - Dimitri Panagopoulos Abrahamsson
, June-Soo Park, Randolph R. Singh
, Marina Sirota, Tracey J. Woodruff:
Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards. 2718-2727 - Christos A. Nicolaou
, Ian A. Watson, Mark Lemasters, Thierry Masquelin, Ji-Bo Wang:
Context Aware Data-Driven Retrosynthetic Analysis. 2728-2738 - Weikaixin Kong
, Xinyu Tu, Weiran Huang, Yang Yang
, Zhengwei Xie, Zhuo Huang
:
Prediction and Optimization of NaV1.7 Sodium Channel Inhibitors Based on Machine Learning and Simulated Annealing. 2739-2753 - Yanxing Wang
, Jianxing Hu
, Junyong Lai
, Yibo Li
, Hongwei Jin, Li He Zhang, Liang Ren Zhang, Zhenming Liu
:
TF3P: Three-Dimensional Force Fields Fingerprint Learned by Deep Capsular Network. 2754-2765 - Fangqiang Zhu
, Xiaohua Zhang
, Jonathan E. Allen
, Derek Jones, Felice C. Lightstone:
Binding Affinity Prediction by Pairwise Function Based on Neural Network. 2766-2772 - Yuting Xu
, Deeptak Verma, Robert P. Sheridan
, Andy Liaw, Junshui Ma, Nicholas M. Marshall, John McIntosh, Edward C. Sherer
, Vladimir Svetnik, Jennifer M. Johnston
:
Deep Dive into Machine Learning Models for Protein Engineering. 2773-2790 - Hussein Hassan-Harrirou, Ce Zhang, Thomas Lemmin
:
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks. 2791-2802 - Atsushi Tokuhisa
, Ryo Kanada
, Shuntaro Chiba
, Kei Terayama
, Yuta Isaka, Biao Ma
, Narutoshi Kamiya
, Yasushi Okuno:
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. 2803-2818 - María Gálvez-Llompart
, Jorge Gálvez
, Fernando Rey
, German Sastre
:
Identification of New Templates for the Synthesis of BEA, BEC, and ISV Zeolites Using Molecular Topology and Monte Carlo Techniques. 2819-2829 - Ulf Norinder
, Ola Spjuth
, Fredrik Svensson
:
Using Predicted Bioactivity Profiles to Improve Predictive Modeling. 2830-2837 - Rachael A. Mansbach
, Inga V. Leus
, Jitender Mehla, Cesar A. López, John K. Walker, Valentin V. Rybenkov
, Nicolas W. Hengartner, Helen I. Zgurskaya
, S. Gnanakaran:
Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. 2838-2847 - Benedict W. J. Irwin
, Julian R. Levell
, Thomas M. Whitehead
, Matthew D. Segall
, Gareth John Conduit:
Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data. 2848-2857 - Ya Chen
, Neann Mathai
, Johannes Kirchmair
:
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands. 2858-2875 - Anna M. Hiszpanski
, Brian Gallagher
, Karthik Chellappan, Peggy Li, Shusen Liu, Hyojin Kim, Jinkyu Han
, Bhavya Kailkhura, David J. Buttler, Thomas Yong-Jin Han
:
Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge. 2876-2887 - Franziska Kruger
, Nikolas Fechner
, Nikolaus Stiefl
:
Automated Identification of Chemical Series: Classifying like a Medicinal Chemist. 2888-2902 - Mahendra Awale
, Sereina Riniker
, Christian Kramer:
Matched Molecular Series Analysis for ADME Property Prediction. 2903-2914 - Ferruccio Palazzesi
, Markus R. Hermann
, Marc A. Grundl, Alexander Pautsch, Daniel Seeliger
, Christofer S. Tautermann
, Alexander Weber
:
BIreactive: A Machine-Learning Model to Estimate Covalent Warhead Reactivity. 2915-2923 - Bishnu Thapa
, Jon Erickson, Krishnan Raghavachari
:
Quantum Mechanical Investigation of Three-Dimensional Activity Cliffs Using the Molecules-in-Molecules Fragmentation-Based Method. 2924-2938 - Anhui Wang, Yuebin Zhang, Huiying Chu, Chenyi Liao
, Zhichao Zhang
, Guohui Li
:
Higher Accuracy Achieved for Protein-Ligand Binding Pose Prediction by Elastic Network Model-Based Ensemble Docking. 2939-2950 - Dragos Horvath
, Gilles Marcou
, Alexandre Varnek
:
"Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry. 2951-2965 - Fabián Avila-Salas, Rafael I. González
, Paulina L. Ríos, Ingrid Araya-Durán, María B. Camarada
:
Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles. 2966-2976 - Vigneshwari Subramanian
, Ekaterina Ratkova, David Palmer
, Ola Engkvist
, Maxim V. Fedorov, Antonio Llinàs
:
Multisolvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors. 2977-2988 - Peter A. Hunt
, Layla Hosseini-Gerami
, Tomas Chrien, Jeffrey Plante
, David J. Ponting
, Matthew D. Segall
:
Predicting pKa Using a Combination of Semi-Empirical Quantum Mechanics and Radial Basis Function Methods. 2989-2997 - Yue Zhao, Agnivo Gosai
, Kyungho Kang, Pranav Shrotriya:
Multiscale Modeling Reveals the Cause of Surface Stress Change on Microcantilevers Due to Alkanethiol SAM Adsorption. 2998-3008 - Irene Luque Ruiz
, Miguel Ángel Gómez-Nieto
:
Prototype Selection Method Based on the Rivality and Reliability Indexes for the Improvement of the Classification Models and External Predictions. 3009-3021 - Fan Yang
, Haixia Lu
, Wanqiang Liu
, Hu Zhou
:
Understanding the Contributions of Microscopic Heat Transfer to Thermal Conductivities of Liquid Aldehydes and Ketones by Molecular Dynamics Simulation. 3022-3029 - Florian Hofer, Johannes Kraml, Ursula Kahler, Anna S. Kamenik
, Klaus R. Liedl
:
Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. 3030-3042 - Raquel Yanes-Rodríguez
, Daniel J. Arismendi-Arrieta
, Rita Prosmiti
:
He Inclusion in Ice-like and Clathrate-like Frameworks: A Benchmark Quantum Chemistry Study of Guest-Host Interactions. 3043-3056 - Nguyen Quoc Thai, Panagiotis E. Theodorakis
, Mai Suan Li
:
Fast Estimation of the Blood-Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane. 3057-3067 - Tadeo E. Saldaño
, Victor M. Freixas, Silvio C. E. Tosatto
, Gustavo D. Parisi, Sebastian Fernandez Alberti
:
Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis. 3068-3080 - Parker Ladd Bremer, Danna De Boer, Walter Alvarado, Xavier Martinez, Eric J. Sorin
:
Overcoming the Heuristic Nature of k-Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes. 3081-3092 - Ivan Syzonenko
, Joshua L. Phillips
:
Accelerated Protein Folding Using Greedy-Proximal A. 3093-3104 - Santanu Santra, Madhurima Jana
:
Insights into the Sensitivity of Arginine Concentration to Preserve the Folded Form of Insulin Monomer under Thermal Stress. 3105-3119 - Maximilian Kuhn
, Stuart Firth-Clark, Paolo Tosco
, Antonia S. J. S. Mey, Mark Mackey
, Julien Michel:
Assessment of Binding Affinity via Alchemical Free-Energy Calculations. 3120-3130 - Richard Bradshaw
, Jacek Dziedzic
, Chris-Kriton Skylaris
, Jonathan W. Essex
:
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields? 3131-3144 - Benedetta Righino
, Manuela Bozzi, Davide Pirolli
, Francesca Sciandra
, Maria Giulia Bigotti
, Andrea Brancaccio
, Maria Cristina De Rosa
:
Identification and Modeling of a GT-A Fold in the α-Dystroglycan Glycosylating Enzyme LARGE1. 3145-3156 - Massimiliano Anselmi
, Paolo Calligari
, Jochen S. Hub
, Marco Tartaglia
, Gianfranco Bocchinfuso, Lorenzo Stella
:
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. 3157-3171 - Mohammed Benabderrahmane, Ronan Bureau
, Anne Sophie Voisin-Chiret
, Jana Sopkova-de Oliveira Santos
:
Insights into Mcl-1 Conformational States and Allosteric Inhibition Mechanism from Molecular Dynamics Simulations, Enhanced Sampling, and Pocket Crosstalk Analysis. 3172-3187 - Jigneshkumar Dahyabhai Prajapati
, Crystal Mele, Mehmet Alphan Aksoyoglu
, Mathias Winterhalter
, Ulrich Kleinekathöfer
:
Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field. 3188-3203 - Matías A. Zúñiga, Pilar A. Vásquez, Gonzalo A. Jaña
, José L. Guzmán, Joel B. Alderete, Verónica A. Jiménez
:
Mechanism-Based Rational Discovery and In Vitro Evaluation of Novel Microtubule Stabilizing Agents with Non-Taxol-Competitive Activity. 3204-3213 - Dan Teng
, Jianhui Chen, Dongping Li, Zengrui Wu
, Weihua Li
, Yun Tang
, Guixia Liu
:
Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators. 3214-3230 - Suqing Zheng, Jun Xiong, Yibing Wang, Guang Liang, Yong Xu, Fu Lin
:
Quantitative Prediction of Hemolytic Toxicity for Small Molecules and Their Potential Hemolytic Fragments by Machine Learning and Recursive Fragmentation Methods. 3231-3245 - Jinsol Yang, Sohee Kwon
, Sang-Hun Bae, Kyoung Mii Park, Changsik Yoon, Ji-Hyun Lee, Chaok Seok
:
GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds. 3246-3254 - Shengjie Liu, Xinyu Zhou, Minglei Li, Wenfeng Zhao, Shuxi Zhou, Keguang Cheng
, Qinglong Xu
, Caiping Chen, Xiaoan Wen
, Hongbin Sun
, Haoliang Yuan
:
Discovery of Ubiquitin-Specific Protease 7 (USP7) Inhibitors with Novel Scaffold Structures by Virtual Screening, Molecular Dynamics Simulation, and Biological Evaluation. 3255-3264 - Wenfeng Zhao, Muya Xiong
, Xiaojing Yuan, Minjun Li, Hongbin Sun
, Yechun Xu
:
In Silico Screening-Based Discovery of Novel Inhibitors of Human Cyclic GMP-AMP Synthase: A Cross-Validation Study of Molecular Docking and Experimental Testing. 3265-3276 - Junmei Wang
:
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study. 3277-3286 - Gudong Li, Wei Zhang, Yuting Xie, Yang Li, Rao Cao, Guojun Zheng, Niu Huang
, Yu Zhou
:
Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. 3287-3294 - Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu
:
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. 3295-3303 - Avinash Mishra
, Rohit Bansal, Shravan Sreenivasan, Rozaleen Dash, Srishti Joshi
, Richa Singh, Anurag S. Rathore
, Gaurav Goel
:
Structure-Based Design of Small Peptide Ligands to Inhibit Early-Stage Protein Aggregation Nucleation. 3304-3314 - Anupam Banerjee
, Pralay Mitra
:
Estimating the Effect of Single-Point Mutations on Protein Thermodynamic Stability and Analyzing the Mutation Landscape of the p53 Protein. 3315-3323
Volume 60, Number 7, July 2020
- Cynthia J. Burrows
, Jiaxing Huang
, Shu Wang
, Hyun Jae Kim
, Gerald J. Meyer, Kirk Schanze
, T. Randall Lee, Jodie L. Lutkenhaus
, David Kaplan
, Christopher Jones
, Carolyn R. Bertozzi, Laura Kiessling, Mary Beth Mulcahy, Craig Lindsley, M. G. Finn, Joel D. Blum, Prashant Kamat, Wonyong Choi, Shane Snyder, Courtney Aldrich, Stuart Rowan, Bin Liu, Dennis Liotta, Paul S. Weiss, Deqing Zhang, Krishna N. Ganesh, Harry A. Atwater, J. Justin Gooding, David T. Allen, Christopher A. Voigt, Jonathan V. Sweedler, Alanna Schepartz, Vincent Rotello, Sébastien Lecommandoux, Shana J. Sturla, Sharon Hammes-Schiffer
, Jillian Buriak, Jonathan W. Steed, Hongwei Wu, Julie Zimmerman, Bryan Brooks
, Phillip Savage, William Tolman, Thomas F. Hofmann
, Joan F. Brennecke, Thomas A. Holme, Kenneth M. Merz Jr.
, Gustavo Scuseria, William Jorgensen, Gunda I. Georg
, Shaomeng Wang, Philip Proteau, John R. Yates, Peter Stang, Gilbert C. Walker, Marc Hillmyer
, Lynne S. Taylor, Teri W. Odom, Erick Carreira, Kai Rossen, Paul Chirik, Scott J. Miller, Joan-Emma Shea, Anne McCoy, Martin Zanni, Gregory Hartland
, Gregory Scholes, Joseph A. Loo, James Milne, Sarah B. Tegen, Daniel T. Kulp, Julia Laskin:
Confronting Racism in Chemistry Journals. 3325-3327 - Angelica Mazzolari
, Ariane Nunes-Alves
, Habibah A. Wahab
, Rommie E. Amaro
, Zoe Cournia
, Kenneth M. Merz Jr.
:
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. 3328-3330 - Franziska Kruger
, Nikolaus Stiefl
, Gregory A. Landrum
:
rdScaffoldNetwork: The Scaffold Network Implementation in RDKit. 3331-3335 - Philip N. Judson
, Wolf-Dietrich Ihlenfeldt
, Hitesh Patel, Victorien Delannée, Nadya I. Tarasova
, Marc C. Nicklaus
:
Adapting CHMTRN (CHeMistry TRaNslator) for a New Use. 3336-3341 - Phyo Phyo Kyaw Zin
, Alexandre Borrel
, Denis Fourches
:
Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict? 3342-3360 - Koichiro Kato
, Tomohide Masuda, Chiduru Watanabe
, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono
, Hiroshi Ueda, Atsushi Tokuhisa
, Ryo Kanada, Masateru Ohta
, Mitsunori Ikeguchi
, Yasushi Okuno, Kaori Fukuzawa
, Teruki Honma
:
High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning. 3361-3368 - Peter Ertl
:
Identification of Bioisosteric Substituents by a Deep Neural Network. 3369-3375 - Saúl H. Martínez-Treviño
, Víctor Uc-Cetina
, María A. Fernández-Herrera, Gabriel Merino
:
Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data. 3376-3386 - Wesley K. Tatum
, Diego Torrejon, Patrick O'neil, Jonathan W. Onorato
, Anton B. Resing, Sarah Holliday, Lucas Q. Flagg
, David S. Ginger
, Christine K. Luscombe
:
Generalizable Framework for Algorithmic Interpretation of Thin Film Morphologies in Scanning Probe Images. 3387-3397 - Michael E. Fortunato
, Connor W. Coley
, Brian C. Barnes, Klavs F. Jensen
:
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning. 3398-3407 - Xiang Gao
, Farhad Ramezanghorbani
, Olexandr Isayev
, Justin S. Smith, Adrian E. Roitberg
:
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials. 3408-3415 - Jason Ott, Daniel Tan, Tyson Loveless
, William H. Grover
, Philip Brisk:
ChemStor: Using Formal Methods To Guarantee Safe Storage and Disposal of Chemicals. 3416-3422 - M. Farooq Wahab
, Sonia Zulfiqar
, Muhammad Ilyas Sarwar
, Ingo Lieberwirth
:
Facile Solutions to the Problems Associated with Chemical Information and Mathematical Symbolism While Using Machine Translation Tools. 3423-3430 - Noah R. Flynn
, Na Le Dang
, Michael D. Ward, S. Joshua Swamidass
:
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation. 3431-3449 - Douglas E. V. Pires
, David B. Ascher
:
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. 3450-3456 - Georgios A. Tritsaris
, Yiqi Xie
, Alexander M. Rush
, Stephen Carr
, Marios Mattheakis
, Efthimios Kaxiras
:
LAN: A Materials Notation for Two-Dimensional Layered Assemblies. 3457-3462 - Monica A. Silva, Alessandra S. Kiametis
, Werner Treptow
:
Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature. 3463-3471 - Henrique M. Cezar
, Sylvio Canuto
, Kaline Coutinho
:
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method. 3472-3488 - Janet L. Paulsen
, Haoyu S. Yu, Dan Sindhikara, Lingle Wang
, Todd Appleby, Armando G. Villaseñor, Uli Schmitz, Devleena Shivakumar:
Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. 3489-3498 - Ryoma Sasaki
, Yoshihiro Hayashi
, Susumu Kawauchi
:
Acceleration of Liquid-Crystalline Phase Transition Simulations Using Selectively Scaled and Returned Molecular Dynamics. 3499-3507 - Anna S. Kamenik
, Johannes Kraml, Florian Hofer, Franz Waibl, Patrick K. Quoika, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
:
Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. 3508-3517 - Paul C. D. Hawkins
, Stanislaw Wlodek:
Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State. 3518-3533 - Wanlei Wei
, Candide Champion
, Stephen J. Barigye
, Zhaomin Liu, Paul Labute, Nicolas Moitessier
:
Use of Extended-Hückel Descriptors for Rapid and Accurate Predictions of Conjugated Torsional Energy Barriers. 3534-3545 - Tom A. Young
, Razvan Gheorghe
, Fernanda Duarte
:
cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization. 3546-3557 - Sohvi Luukkonen
, Luc Belloni
, Daniel Borgis
, Maximilien Levesque
:
Predicting Hydration Free Energies of the FreeSolv Database of Drug-like Molecules with Molecular Density Functional Theory. 3558-3565 - Samo Lesnik
, Milan Hodoscek
, Urban Bren
, Christoph Stein
, Ana-Nicoleta Bondar
:
Potential Energy Function for Fentanyl-Based Opioid Pain Killers. 3566-3576 - Genoveva Rojas, Ivana Orellana, Roberto Rosales-Rojas, Jennie García-Olivares
, Jeffrey Comer
, Ariela Vergara Jaque
:
Structural Determinants of the Dopamine Transporter Regulation Mediated by G Proteins. 3577-3586 - Hao Li, Yeonsig Nam
, Abbas Salimi, Jin Yong Lee
:
Impact of A2V Mutation and Histidine Tautomerism on Aβ42 Monomer Structures from Atomistic Simulations. 3587-3592 - Ryo Hatada, Koji Okuwaki
, Yuji Mochizuki
, Yuma Handa, Kaori Fukuzawa
, Yuto Komeiji
, Yoshio Okiyama
, Shigenori Tanaka
:
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). 3593-3602 - Yue Zhang
, Hong-Xing Zhang
, Qing-Chuan Zheng
:
In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel. 3603-3615 - Lindy Astl, Gabrielle Stetz, Gennady M. Verkhivker
:
Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction Networks. 3616-3631 - Fei Xiao, Xingyu Song, Peiyi Tian, Mi Gan, Gennady M. Verkhivker
, Guang Hu
:
Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding. 3632-3647 - William H. Coldren
, Svetlana B. Tikunova, Jonathan P. Davis, Steffen Lindert
:
Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach. 3648-3661 - Kaja Bergant Loboda, Matej Janezic
, Martina Stampar
, Bojana Zegura, Metka Filipic, Andrej Perdih
:
Substituted 4, 5′-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα. 3662-3678 - Wei-Xun Zhang, Xiaoyong Pan, Hong-Bin Shen
:
Signal-3L 3.0: Improving Signal Peptide Prediction through Combining Attention Deep Learning with Window-Based Scoring. 3679-3686
Volume 60, Number 8, August 2020
- Zengrui Wu
, Yayuan Peng, Zhuohang Yu, Weihua Li
, Guixia Liu
, Yun Tang
:
NetInfer: A Web Server for Prediction of Targets and Therapeutic and Adverse Effects via Network-Based Inference Methods. 3687-3691 - Irina V. Gushchina, Aleksandra M. Polenova, Dmitry A. Suplatov
, Vytas K. Svedas, Dmitry K. Nilov
:
vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses. 3692-3696 - Enade P. Istyastono
, Muhammad Radifar
, Nunung Yuniarti
, Vivitri Dewi Prasasty, Sudi Mungkasi:
PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS. 3697-3702 - Mariia Radaeva, Xuesen Dong, Artem Cherkasov
:
The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. 3703-3721 - Jack Scantlebury
, Nathan Brown
, Frank von Delft
, Charlotte M. Deane
:
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions. 3722-3730 - Peiyuan Gao
, Xiu Yang, Alexandre M. Tartakovsky:
Learning Coarse-Grained Potentials for Binary Fluids. 3731-3745 - Peng Gao
, Jun Zhang, Qian Peng
, Jie Zhang
, Vassiliki-Alexandra Glezakou
:
General Protocol for the Accurate Prediction of Molecular 13C/1H NMR Chemical Shifts via Machine Learning Augmented DFT. 3746-3754 - Runyu Jing
, Yizhou Li, Li Xue, Fengjuan Liu, Menglong Li, Jiesi Luo
:
autoBioSeqpy: A Deep Learning Tool for the Classification of Biological Sequences. 3755-3764 - Seokho Kang
, Youngchun Kwon, Dongseon Lee, Youn-Suk Choi
:
Predictive Modeling of NMR Chemical Shifts without Using Atomic-Level Annotations. 3765-3769 - Lior Hirschfeld, Kyle Swanson
, Kevin Yang, Regina Barzilay, Connor W. Coley
:
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. 3770-3780 - Christopher M. Baker
, Nathan J. Kidley, Konstantinos Papachristos, Matthew Hotson, Rob Carson, David Gravestock, Martin Pouliot, Jim Harrison, Alan Dowling:
Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry. 3781-3791 - Natasha Kamerlin
, Mickaël G. Delcey
, Sergio Manzetti
, David van der Spoel
:
Toward a Computational Ecotoxicity Assay. 3792-3803 - Joshua Schrier
:
Can One Hear the Shape of a Molecule (from its Coulomb Matrix Eigenvalues)? 3804-3811 - Asma Nazar, Ghulam Abbas
, Syed Sikander Azam
:
Deciphering the Inhibition Mechanism of under Trial Hsp90 Inhibitors and Their Analogues: A Comparative Molecular Dynamics Simulation. 3812-3830 - Bruno Cuevas-Zuviría, Luis Fernández Pacios
:
Analytical Model of Electron Density and Its Machine Learning Inference. 3831-3842 - Johannes Kraml, Florian Hofer, Anna S. Kamenik
, Franz Waibl, Ursula Kahler, Michael Schauperl, Klaus R. Liedl
:
Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. 3843-3853 - N. Arul Murugan
, Robert Zalesny
:
Multiscale Modeling of Two-Photon Probes for Parkinson's Diagnostics Based on Monoamine Oxidase B Biomarker. 3854-3863 - Aishwary T. Shivgan, Jan K. Marzinek
, Roland G. Huber
, Alexander Krah
, Richard H. Henchman
, Paul Matsudaira, Chandra S. Verma
, Peter J. Bond
:
Extending the Martini Coarse-Grained Force Field to N-Glycans. 3864-3883 - Jan-Grimo Sobez, Markus Reiher
:
Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules. 3884-3900 - Mohammad A. Ghattas
, Sara Al Rawashdeh, Noor Atatreh
, Richard A. Bryce
:
How Do Small Molecule Aggregates Inhibit Enzyme Activity? A Molecular Dynamics Study. 3901-3909 - Natesh Singh, Ludovic Chaput, Bruno O. Villoutreix
:
Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein-Protein Interfaces. 3910-3934 - Florencia Klein
, Daniela Cáceres, Mónica A. Carrasco, Juan Carlos Tapia, Julio Caballero
, Jans H. Alzate-Morales
, Sergio Pantano
:
Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. 3935-3943 - Rajas Rao
, Julien Diharce
, Bérénice Dugué, Mariano A. Ostuni
, Frédéric Cadet, Catherine Etchebest
:
Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study. 3944-3957 - Liang Xu
, Liao Y. Chen
:
Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. 3958-3968 - António J. Preto
, Carlos A. V. Barreto
, Salete J. Baptista, José G. de Almeida
, Agostinho Lemos
, André Melo
, M. Natália Dias Soeiro Cordeiro
, Zeynep Kurkcuoglu, Rita Melo
, Irina S. Moreira
:
Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family. 3969-3984 - Rodrigo Aguayo-Ortiz
, Eli Fernández-de Gortari, L. Michel Espinoza-Fonseca
:
Conserved Luminal C-Terminal Domain Dynamically Controls Interdomain Communication in Sarcolipin. 3985-3991 - Jonathan Parkinson
, Ryan Hard, Richard I. Ainsworth
, Nan Li, Wei Wang:
Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression. 3992-4004 - Guido Todde, Ran Friedman
:
Pattern and Dynamics of FLT3 Duplications. 4005-4020 - Takunori Yasuda, Yasuteru Shigeta
, Ryuhei Harada
:
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. 4021-4029 - Christopher M. Siwy
, Bryan M. Delfing, Amy K. Smith, Dmitri K. Klimov
:
Partitioning of Benzoic Acid into 1, 2-Dimyristoyl-sn-glycero-3-phosphocholine and Blood-Brain Barrier Mimetic Bilayers. 4030-4046 - Yusuf Serhat Is, Busecan Aksoydan
, Murat Senturk, Mine Yurtsever
, Serdar Durdagi
:
Integrated Binary QSAR-Driven Virtual Screening and In Vitro Studies for Finding Novel hMAO-B-Selective Inhibitors. 4047-4055 - Vinicius M. Alves
, Stephen J. Capuzzi
, Rodolpho C. Braga
, Daniel Robert Korn, Joshua E. Hochuli
, Kyle H. Bowler, Adam Yasgar
, Ganesha Rai
, Anton Simeonov, Eugene N. Muratov
, Alexey V. Zakharov
, Alexander Tropsha
:
SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. 4056-4063 - Vikash Kumar
, Hannah Hoag
, Safaa Sader, Nicolas Scorese, Haiguang Liu, Chun Wu
:
GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor. 4064-4075 - Cong Shen
, Jiawei Luo, Zihan Lai, Pingjian Ding
:
Multiview Joint Learning-Based Method for Identifying Small-Molecule-Associated MiRNAs by Integrating Pharmacological, Genomics, and Network Knowledge. 4085-4097 - Japheth E. Gado
, Gregg T. Beckham
, Christina M. Payne
:
Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning. 4098-4107 - Joseph M. Jakubowski, Asuka A. Orr, Doan A. Le, Phanourios Tamamis
:
Correction to "Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations". 4108
Volume 60, Number 9, September 2020
- W. Patrick Walters
, Renxiao Wang
:
New Trends in Virtual Screening. 4109-4111 - Dagmar Stumpfe, Jürgen Bajorath
:
Current Trends, Overlooked Issues, and Unmet Challenges in Virtual Screening. 4112-4115 - Eric J. Martin
, Johanna M. Jansen
:
Biased Diversity for Effective Virtual Screening. 4116-4119 - David E. Clark
:
Virtual Screening: Is Bigger Always Better? Or Can Small Be Beautiful? 4120-4123 - Horacio Pérez Sánchez
, Helena den-Haan, Jorge Peña-García, Jesús Lozano-Sánchez, María Encarnación Martínez Moreno, Antonia Sánchez-Pérez, Andrés Muñoz
, Pedro Ruiz-Espinosa, Andreia S. P. Pereira
, Antigoni Katsikoudi, José Antonio Gabaldón Hernández
, Ivana Stojanovic, Antonio Segura Carretero, Andreas G. Tzakos:
DIA-DB: A Database and Web Server for the Prediction of Diabetes Drugs. 4124-4130 - William Mangione
, Zackary Falls
, Gaurav Chopra
, Ram Samudrala:
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. 4131-4136 - Jonathan Fine, Matthew Muhoberac, Guillaume Fraux
, Gaurav Chopra
:
DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening. 4137-4143 - Xin Cindy Yan
, John M. Sanders
, Ying-Duo Gao, Matthew Tudor
, Andrew M. Haidle, Daniel J. Klein, Antonella Converso, Charles A. Lesburg, Yi Zang, Harold B. Wood:
Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery. 4144-4152 - Zoe Cournia
, Bryce K. Allen
, Thijs Beuming, David A. Pearlman
, Brian K. Radak
, Woody Sherman
:
Rigorous Free Energy Simulations in Virtual Screening. 4153-4169 - Joseph A. Morrone
, Jeffrey K. Weber, Tien Huynh, Heng Luo
, Wendy D. Cornell:
Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking Approach. 4170-4179 - Selcuk Korkmaz
:
Deep Learning-Based Imbalanced Data Classification for Drug Discovery. 4180-4190 - Paul Morris
, Rachel St. Clair, William Edward Hahn, Elan Barenholtz:
Predicting Binding from Screening Assays with Transformer Network Embeddings. 4191-4199 - Paul G. Francoeur
, Tomohide Masuda, Jocelyn Sunseri
, Andrew Jia, Richard B. Iovanisci, Ian Snyder, David Ryan Koes
:
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. 4200-4215 - Wenling Ye, Chao Shen, Guo-Li Xiong
, Jun-Jie Ding, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao
:
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. 4216-4230 - Javier Vázquez
, Alessandro Deplano, Albert Herrero
, Enric Gibert, Enric Herrero
, F. Javier Luque
:
Assessing the Performance of Mixed Strategies To Combine Lipophilic Molecular Similarity and Docking in Virtual Screening. 4231-4245 - Stanislaw Jastrzebski, Maciej Szymczak, Agnieszka Pocha, Stefan Mordalski
, Jacek Tabor, Andrzej J. Bojarski
, Sabina Podlewska
:
Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening. 4246-4262 - Viet-Khoa Tran-Nguyen
, Célien Jacquemard, Didier Rognan
:
LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening. 4263-4273 - Christoph Grebner
, Erik Malmerberg
, Andrew Shewmaker
, José Batista
, Anthony Nicholls
, Jens Sadowski
:
Virtual Screening in the Cloud: How Big Is Big Enough? 4274-4282 - Lindsey Burggraaff
, Eelke B. Lenselink, Willem Jespers
, Jesper E. van Engelen, Brandon J. Bongers
, Marina Gorostiola González
, Rongfang Liu, Holger H. Hoos, Herman W. T. van Vlijmen
, Adriaan P. IJzerman, Gerard J. P. van Westen
:
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. 4283-4295 - Ann E. Cleves
, Ajay N. Jain
:
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket. 4296-4310 - Phani Ghanakota
, Pieter H. Bos
, Kyle D. Konze, Joshua Staker
, Gabriel Marques, Kyle Marshall, Karl Leswing, Robert Abel, Sathesh Bhat
:
Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization. 4311-4325 - Siduo Jiang, Miklos Feher, Christopher I. Williams, Brian Cole, David E. Shaw
:
AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. 4326-4338 - Yan Li
, Yaping Sun, Yunpeng Song, Dongcheng Dai
, Zhixiong Zhao, Qing Zhang, Wenge Zhong, Liaoyuan A. Hu, Yingli Ma, Xun Li
, Renxiao Wang
:
Fragment-Based Computational Method for Designing GPCR Ligands. 4339-4349 - Hao Liang
, Hongbo Liu, Yi Kuang, Limin Chen, Min Ye
, Luhua Lai
:
Discovery of Targeted Covalent Natural Products against PLK1 by Herb-Based Screening. 4350-4358 - Yan Li
, Yingduo Gao, M. Katharine Holloway, Renxiao Wang
:
Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. 4359-4375 - Francois Berenger
, Yoshihiro Yamanishi:
Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included. 4376-4387 - Lin Wei
, Wuqiang Wen, Li Rao, Yunyuan Huang, Mengting Lei, Kai Liu, Saiya Hu, Rongrong Song, Yanliang Ren
, Jian Wan
:
Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation. 4388-4402 - Kara J. Cutrona, Ana S. Newton, Stefan G. Krimmer
, Julian Tirado-Rives
, William L. Jorgensen
:
Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2. 4403-4415
Volume 60, Number 10, October 2020
- W. Patrick Walters:
Code Sharing in the Open Science Era. 4417-4420 - David A. Winkler
:
Ligand Entropy Is Hard but Should Not Be Ignored. 4421-4423 - Patrick G. Sahrmann
, Patrick H. Donnan
, Kenneth M. Merz Jr.
, Steven O. Mansoorabadi, Douglas C. Goodwin
:
MRP.py: A Parametrizer of Post-Translationally Modified Residues. 4424-4428 - Zhiwei Feng
, Maozi Chen
, Mingzhe Shen
, Tianjian Liang, Hui Chen, Xiang-Qun Xie
:
Pain-CKB, A Pain-Domain-Specific Chemogenomics Knowledgebase for Target Identification and Systems Pharmacology Research. 4429-4435 - Marley L. Samways
, Hannah E. Bruce Macdonald
, Jonathan W. Essex
:
grand: A Python Module for Grand Canonical Water Sampling in OpenMM. 4436-4441 - Pedro B. P. S. Reis, Diogo Vila-Viçosa
, Walter Rocchia
, Miguel Machuqueiro
:
PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. 4442-4448 - Todd J. Wills
, Dmitrii A. Polshakov, Matthew C. Robinson, Alpha A. Lee:
Impact of Chemist-In-The-Loop Molecular Representations on Machine Learning Outcomes. 4449-4456 - Alex D. Casey
, Steven F. Son, Ilias Bilionis
, Brian C. Barnes:
Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks. 4457-4473 - Zhongliang Guo
, Stephen Wu
, Mitsuru Ohno
, Ryo Yoshida
:
Bayesian Algorithm for Retrosynthesis. 4474-4486 - Paul Maragakis, Hunter M. Nisonoff, Brian Cole, David E. Shaw
:
A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. 4487-4496 - Lei Deng, Yideng Cai
, Wenhao Zhang
, Wenyi Yang, Bo Gao, Hui Liu
:
Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity. 4497-4505 - Martijn Oldenhof
, Adam Arany, Yves Moreau
, Jaak Simm:
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning. 4506-4517 - Callum J. Court
, Batuhan Yildirim
, Apoorv Jain, Jacqueline M. Cole
:
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning. 4518-4535 - Lewis J. Martin
, Michael T. Bowen:
Comparing Fingerprints for Ligand-Based Virtual Screening: A Fast and Scalable Approach for Unbiased Evaluation. 4536-4545 - Lewis H. Mervin
, Avid M. Afzal, Ola Engkvist
, Andreas Bender
:
Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions. 4546-4559 - David J. Ponting
, Ruud van Deursen, Martin A. Ott
:
Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints. 4560-4568 - Hao Tian
, Peng Tao
:
ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. 4569-4581 - Domenico Alberga
, Nicola Gambacorta
, Daniela Trisciuzzi, Fulvio Ciriaco
, Nicola Amoroso, Orazio Nicolotti
:
De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization. 4582-4593 - Huaipan Jiang
, Mengran Fan
, Jian Wang
, Anup Sarma
, Shruti Mohanty
, Nikolay V. Dokholyan
, Mehrdad Mahdavi
, Mahmut T. Kandemir
:
Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. 4594-4602 - Xiting Wang
, Meng Liu, Lan Zhang, Yun Wang, Yu Li, Tao Lu:
Optimizing Pharmacokinetic Property Prediction Based on Integrated Datasets and a Deep Learning Approach. 4603-4613 - Suman K. Chakravarti
:
Reason Vectors: Abstract Representation of Chemistry-Biology Interaction Outcomes, for Reasoning and Prediction. 4614-4628 - Luka Stojanovic, Milos Popovic, Nebojsa Tijanic, Goran Rakocevic
, Marko Kalinic
:
Improved Scaffold Hopping in Ligand-Based Virtual Screening Using Neural Representation Learning. 4629-4639 - Xingye Chen, Wuchen Xie, Yan Yang, Yi Hua, Guomeng Xing, Li Liang, Chenglong Deng, Yuchen Wang, Yuanrong Fan, Haichun Liu, Tao Lu, Yadong Chen
, Yanmin Zhang
:
Discovery of Dual FGFR4 and EGFR Inhibitors by Machine Learning and Biological Evaluation. 4640-4652 - Anthony Difranzo
, Robert P. Sheridan
, Andy Liaw, Matthew Tudor
:
Nearest Neighbor Gaussian Process for Quantitative Structure-Activity Relationships. 4653-4663 - Lindsey Burggraaff
, Amber van Veen, Chi Chung Lam, Herman W. T. van Vlijmen
, Adriaan P. IJzerman, Gerard J. P. van Westen
:
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. 4664-4672 - Himaghna Bhattacharjee
, Dionisios G. Vlachos
:
Thermochemical Data Fusion Using Graph Representation Learning. 4673-4683 - Ruimin Ma
, Tengfei Luo
:
PI1M: A Benchmark Database for Polymer Informatics. 4684-4690 - Kaveh Kavousi
, Mojtaba Bagheri
, Saman Behrouzi
, Safar Vafadar, Fereshteh Fallah Atanaki
, Bahareh Teimouri Lotfabadi, Shohreh Ariaeenejad
, Abbas Shockravi, Ali Akbar Moosavi-Movahedi
:
IAMPE: NMR-Assisted Computational Prediction of Antimicrobial Peptides. 4691-4701 - Tyler B. Hughes
, Na Le Dang
, Ayush Kumar, Noah R. Flynn
, S. Joshua Swamidass
:
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. 4702-4716 - Bashir Akhlaq Akhoon, Sushil Choudhary, Harshita Tiwari, Ajay Kumar
, Manas Ranjan Barik, Laxmi Rathor, Rakesh Pandey, Amit Nargotra
:
Discovery of a New Donepezil-like Acetylcholinesterase Inhibitor for Targeting Alzheimer's Disease: Computational Studies with Biological Validation. 4717-4729 - Carmen Esposito
, Shuzhe Wang
, Udo E. W. Lange
, Frank Oellien
, Sereina Riniker
:
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. 4730-4749 - Shao Hua Lu, Hong Lin Zhai
, Bing Qiang Zhao, Bo Yin
, Ling Zhu:
Novel Approach to the Analysis of Chemical Third-Order Data. 4750-4756 - James A. Lumley
, Prashant V. Desai
, Ji-Bo Wang, Suntara Cahya, Hongzhou Zhang
:
The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization. 4757-4771 - Octav Caldararu, Rukmankesh Mehra
, Tom L. Blundell, Kasper P. Kepp
:
Systematic Investigation of the Data Set Dependency of Protein Stability Predictors. 4772-4784 - Masakazu Nakadai, Shuta Tomida
:
Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein-Protein Interactions. 4785-4790 - Antonio Llinàs
, Ioana Oprisiu, Alex Avdeef
:
Findings of the Second Challenge to Predict Aqueous Solubility. 4791-4803 - Stefano Costanzi
, Charlotte K. Slavick, Brent O. Hutcheson, Gregory D. Koblentz, Richard T. Cupitt:
Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis. 4804-4816 - Tárcius N. Ramos
, Sylvio Canuto
, Benoît Champagne
:
Unraveling the Electric Field-Induced Second Harmonic Generation Responses of Stilbazolium Ion Pairs Complexes in Solution Using a Multiscale Simulation Method. 4817-4826 - Krishna Gopal Chattaraj
, Sandip Paul
:
Investigation on the Mechanisms of Synchronous Interaction of K3Cit with Melamine and Uric Acid That Avoids the Formation of Large Clusters. 4827-4844 - Josiah Roberts, Yang Song, Mark Crocker
, Chad Risko
:
A Genetic Algorithmic Approach to Determine the Structure of Li-Al Layered Double Hydroxides. 4845-4855 - Masoumeh Mousavi
, Elham H. Fini
:
Non-Covalent π-Stacking Interactions between Asphaltene and Porphyrin in Bitumen. 4856-4866 - Junichi Higo
, Takeshi Kawabata
, Ayumi Kusaka, Kota Kasahara
, Narutoshi Kamiya
, Ikuo Fukuda, Kentaro Mori, Yutaka Hata, Yoshifumi Fukunishi, Haruki Nakamura:
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. 4867-4880 - Kenneth Goossens
, Berthold Wroblowski
, Cassiano Langini
, Herman van Vlijmen
, Amedeo Caflisch
, Hans De Winter
:
Assessment of the Fragment Docking Program SEED. 4881-4893 - Daniel Zaidman, Jaime Prilusky, Nir London
:
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. 4894-4903 - Nobuaki Kikkawa
, Seiji Kajita, Kensuke Takechi
:
Self-Learning Molecular Design for High Lithium-Ion Conductive Ionic Liquids using Maze Game. 4904-4911 - Mueed Ur Rahman, Ashfaq Ur Rehman
, Hao Liu
, Hai-Feng Chen
:
Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins. 4912-4923 - Rahul Prabhu
, Meera Sitharam, Aysegul Ozkan, Ruijin Wu:
Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity. 4924-4957 - Ignacio Migliaro
, Thomas R. Cundari
:
Density Functional Study of Methane Activation by Frustrated Lewis Pairs with Group 13 Trihalides and Group 15 Pentahalides and a Machine Learning Analysis of Their Barrier Heights. 4958-4966 - Bin Chong
, Yingguang Yang
, Chenguang Zhou, Qiaojing Huang
, Zhirong Liu
:
Ensemble-Based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small-Molecule Ligands. 4967-4974 - Jianguo Li
, Roger Beuerman, Chandra S. Verma
:
Dissecting the Molecular Mechanism of Colistin Resistance in mcr-1 Bacteria. 4975-4984 - Jingyuan Zhuang, Fan Zhang, Jingwei Zhou
, Wenbin Deng, Ruibo Wu
:
Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases. 4985-4994 - Nivedita Dutta
, Joanna Sarzynska
, Ansuman Lahiri
:
Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space. 4995-5002 - Pablo Herrera-Nieto
, Adrià Pérez
, Gianni De Fabritiis
:
Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. 5003-5010 - Nabil Abid
, Daniele Pietrucci
, Marco Salemi, Giovanni Chillemi
:
New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations. 5011-5025 - Junhao Li, Yang Zhou
, Yun Tang
, Weihua Li
, Yaoquan Tu
:
Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations. 5026-5035 - Federica Cossu
, Luca Sorrentino
, Elisa Fagnani, Mattia Zaffaroni
, Mario Milani, Toni Giorgino
, Eloise Mastrangelo
:
Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly. 5036-5044 - Grazia Cottone
, Letizia Chiodo
, Luca Maragliano
:
Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. 5045-5056 - Anupam Mondal
, Arnab Bhattacherjee
:
Mechanism of Dynamic Binding of Replication Protein A to ssDNA. 5057-5069 - Daisuke Miyata
, Takakazu Nakabayashi
, Shin-ichi Morita
:
Automatic Determination of the Sequential Order of Dynamic Data and Its Application to Vibrational Spectroscopy. 5070-5079 - Olivier Sheik Amamuddy
, Gennady M. Verkhivker
, Özlem Tastan Bishop
:
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. 5080-5102 - Jakob Schneider
, Ksenia Korshunova
, Zeineb Si Chaib
, Alejandro Giorgetti
, Mercedes Alfonso-Prieto
, Paolo Carloni
:
Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. 5103-5116 - Joshua W. Wilkerson
, Addison K. Smith
, Kristen M. Wilding
, Bradley C. Bundy
, Thomas A. Knotts
:
The Effects of p-Azidophenylalanine Incorporation on Protein Structure and Stability. 5117-5125 - Chenchen Wu, Shengtang Liu, Shitong Zhang, Zaixing Yang
:
Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation. 5126-5131 - Yan Zhang, Zhanyi Lin, Ying Fang, Jianhua Wu
:
Prediction of Catch-Slip Bond Transition of Kindlin2/β3 Integrin via Steered Molecular Dynamics Simulation. 5132-5141 - Galo E. Balatti
, Carmen Domene
, M. Florencia Martini
, Mónica Pickholz
:
Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains. 5142-5152 - Xiaocong Wang
, Lihua Bie
, Junwen Fei
, Jun Gao
:
Insights into the Loop at the E-Selectin Binding Site: From Open to Close Conformation. 5153-5161 - Angelo Spadaro
, Livia Basile
, Matteo Pappalardo
, Carmela Bonaccorso
, Marco Rao
, Simone Ronsisvalle
, Giuseppe Granata
, Salvatore Guccione
:
Quantum Chemical and Molecular Dynamics Studies of MUC1 Calix[4, 8]arene Scaffold Based Anticancer Vaccine Candidates. 5162-5171 - Jordi Llopis-Lorente, Julio Gomis-Tena
, Jordi Cano
, Lucía Romero, Javier Saiz, Beatriz Trénor:
In Silico Classifiers for the Assessment of Drug Proarrhythmicity. 5172-5187 - Jean-Rémy Marchand
, Tim Knehans, Amedeo Caflisch
, Andreas Vitalis
:
An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. 5188-5202 - Holli-Joi Sullivan
, Brian Chen
, Chun Wu
:
Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex. 5203-5224 - Jianyu Li
, Aurélien F. A. Moumbock
, Stefan Günther
:
Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins. 5225-5233 - Michael L. Drummond
, Andrew Henry, Huifang Li, Christopher I. Williams
:
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies. 5234-5254 - Yang Li, Baofu Qiao
, Monica Olvera de la Cruz
:
Protein Surface Printer for Exploring Protein Domains. 5255-5264 - Paolo Moretti
, Paolo Mariani
, Maria Grazia Ortore
, Nicoletta Plotegher
, Luigi Bubacco
, Mariano Beltramini, Francesco Spinozzi
:
Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α-Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X-ray Scattering and Variational Bayesian Weighting. 5265-5281 - Shayma El-Atawneh
, Shira Hirsch, Rivka Hadar, Joseph Tam, Amiram Goldblum
:
Correction to Prediction and Experimental Confirmation of Novel Peripheral Cannabinoid-1 Receptor Antagonists. 5282
Volume 60, Number 11, November 2020
- Kira A. Armacost
, Sereina Riniker
, Zoe Cournia
:
Exploring Novel Directions in Free Energy Calculations. 5283-5286 - Amy Y. Shih
, Michael D. Hack
, Taraneh Mirzadegan:
Impact of Protein Preparation on Resulting Accuracy of FEP Calculations. 5287-5289 - Tharindu Senapathi
, Miroslav Suruzhon
, Christopher B. Barnett
, Jonathan W. Essex
, Kevin J. Naidoo
:
BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations. 5290-5295 - Hsu-Chun Tsai
, Yujun Tao
, Tai-Sung Lee
, Kenneth M. Merz Jr.
, Darrin M. York
:
Validation of Free Energy Methods in AMBER. 5296-5300 - Haochuan Chen
, Julio D. C. Maia, Brian K. Radak
, David J. Hardy
, Wensheng Cai
, Christophe Chipot
, Emad Tajkhorshid
:
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. 5301-5307 - Lin Frank Song
, Kenneth M. Merz Jr.
:
Evolution of Alchemical Free Energy Methods in Drug Discovery. 5308-5318 - Julia Gebhardt, Matthias Kiesel, Sereina Riniker
, Niels Hansen
:
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. 5319-5330 - Jenke Scheen, Wilson Wu, Antonia S. J. S. Mey, Paolo Tosco
, Mark Mackey
, Julien Michel
:
Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies. 5331-5339 - Surl-Hee Ahn
, Benjamin R. Jagger
, Rommie E. Amaro
:
Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. 5340-5352 - Ercheng Wang
, Hui Liu
, Junmei Wang
, Gaoqi Weng, Huiyong Sun
, Zhe Wang
, Yu Kang, Tingjun Hou
:
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. 5353-5365 - Haohao Fu
, Haochuan Chen
, Xin'ao Wang, Hao Chai, Xueguang Shao
, Wensheng Cai
, Christophe Chipot
:
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape. 5366-5374 - W. F. Drew Bennett
, Stewart He, Camille L. Bilodeau
, Derek Jones, Delin Sun, Hyojin Kim, Jonathan E. Allen
, Felice C. Lightstone, Helgi I. Ingólfsson
:
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. 5375-5381 - Hiraku Oshima
, Suyong Re
, Yuji Sugita
:
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method. 5382-5394 - Jan Walther Perthold
, Drazen Petrov
, Chris Oostenbrink
:
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). 5395-5406 - Gerhard König
, Nina Glaser
, Benjamin Schroeder
, Alzbeta Kubincová
, Philippe H. Hünenberger
, Sereina Riniker
:
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. 5407-5423 - Anita Plazinska
, Wojciech Plazinski
:
Chirality Effects in Biomolecular Systems: Calculation of the Relative Free Energies by Molecular Dynamics Simulations. 5424-5436 - Zheng Zheng
, Oleg Y. Borbulevych, Hao Liu, Jianpeng Deng, Roger I. Martin, Lance M. Westerhoff
:
MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. 5437-5456 - Christina E. M. Schindler
, Hannah M. Baumann, Andreas Blum, Dietrich Böse
, Hans-Peter Buchstaller
, Lars Burgdorf, Daniel Cappel
, Eugene Chekler, Paul Czodrowski
, Dieter Dorsch, Merveille K. I. Eguida, Bruce Follows, Thomas Fuchß, Ulrich Grädler
, Jakub Gunera, Theresa Johnson, Catherine Jorand Lebrun, Srinivasa Karra, Markus Klein, Tim Knehans, Lisa Koetzner, Mireille Krier
, Matthias Leiendecker, Birgitta Leuthner, Liwei Li, Igor Mochalkin, Djordje Musil, Constantin Neagu, Friedrich Rippmann
, Kai Schiemann, Robert Schulz, Thomas Steinbrecher, Eva-Maria Tanzer, Andrea Unzue Lopez, Ariele Viacava Follis, Ansgar Wegener, Daniel Kuhn
:
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects. 5457-5474 - Samo Lesnik, Milan Hodoscek
, Barbara Podobnik, Janez Konc
:
Loop Grafting between Similar Local Environments for Fc-Silent Antibodies. 5475-5486 - Ellen E. Guest, Steven A. Oatley, Simon J. F. Macdonald, Jonathan D. Hirst
:
Molecular Simulation of αvβ6 Integrin Inhibitors. 5487-5498 - Jorge Enrique Hernández González
, Lilian Hernández Alvarez, Vitor B. P. Leite
, Pedro Geraldo Pascutti
:
Water Bridges Play a Key Role in Affinity and Selectivity for Malarial Protease Falcipain-2. 5499-5512 - Kenneth Goossens
, Rui P. P. Neves
, Pedro Alexandrino Fernandes
, Hans De Winter
:
A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. 5513-5528 - Joan F. Gilabert
, Oriol Gracia Carmona
, Anders Hogner, Victor Guallar
:
Combining Monte Carlo and Molecular Dynamics Simulations for Enhanced Binding Free Energy Estimation through Markov State Models. 5529-5539 - Arghya Chakravorty
, Jonathan Higham, Richard H. Henchman
:
Entropy of Proteins Using Multiscale Cell Correlation. 5540-5551 - Till Siebenmorgen, Martin Zacharias
:
Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling. 5552-5562 - Francesca Deflorian
, Laura Pérez-Benito
, Eelke B. Lenselink
, Miles Congreve
, Herman W. T. van Vlijmen
, Jonathan S. Mason, Chris de Graaf
, Gary Tresadern
:
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. 5563-5579 - Alexander D. Wade
, David J. Huggins
:
Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. 5580-5594 - Tai-Sung Lee
, Bryce K. Allen
, Timothy J. Giese, Zhenyu Guo, Pengfei Li, Charles Lin, T. Dwight McGee Jr., David A. Pearlman, Brian K. Radak
, Yujun Tao
, Hsu-Chun Tsai
, Huafeng Xu
, Woody Sherman
, Darrin M. York
:
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. 5595-5623 - Saara Lautala
, Riccardo Provenzani
, Artturi Koivuniemi
, Waldemar Kulig
, Virpi Talman
, Tomasz Róg
, Raimo K. Tuominen
, Jari Yli-Kauhaluoma
, Alex Bunker
:
Rigorous Computational Study Reveals What Docking Overlooks: Double Trouble from Membrane Association in Protein Kinase C Modulators. 5624-5633
Volume 60, Number 12, December 2020
- Issue Editorial Masthead.
- Issue Publication Information.
- Kenneth M. Merz Jr.
, Gianni De Fabritiis
, Guo-Wei Wei
:
Generative Models for Molecular Design. 5635-5636 - Maxime Langevin
, Hervé Minoux, Maximilien Levesque
, Marc Bianciotto:
Scaffold-Constrained Molecular Generation. 5637-5646 - Ke Yu
, Shyam Visweswaran, Kayhan Batmanghelich:
Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space. 5647-5657 - Jacques Boitreaud
, Vincent Mallet
, Carlos G. Oliver
, Jérôme Waldispühl
:
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery. 5658-5666 - Mostafa Karimi, Shaowen Zhu, Yue Cao, Yang Shen
:
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. 5667-5681 - Kaifu Gao, Duc Duy Nguyen, Meihua Tu, Guo-Wei Wei
:
Generative Network Complex for the Automated Generation of Drug-like Molecules. 5682-5698 - Silvia Amabilino, Peter Pogány
, Stephen D. Pickett
, Darren V. S. Green:
Guidelines for Recurrent Neural Network Transfer Learning-Based Molecular Generation of Focused Libraries. 5699-5713 - Wenhao Gao
, Connor W. Coley
:
The Synthesizability of Molecules Proposed by Generative Models. 5714-5723 - Adrian J. Mulholland
, Rommie E. Amaro
:
COVID19 - Computational Chemists Meet the Moment. 5724-5726 - Aled M. Edwards
:
What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen? 5727-5729 - Miquel Duran-Frigola
, Martino Bertoni
, Roi Blanco, Víctor Martínez, Eduardo Pauls
, Víctor Alcalde, Gemma Turon
, Núria Villegas
, Adrià Fernández-Torras, Carles Pons
, Lidia Mateo
, Oriol Guitart-Pla, Pau Badia-i-Mompel
, Aleix Gimeno, Nicolas Soler, Isabelle Brun-Heath
, Hugo Zaragoza, Patrick Aloy:
Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs. 5730-5734 - Chi Xu, Zunhui Ke, Chuandong Liu, Zhihao Wang, Denghui Liu, Lei Zhang, Jingning Wang, Wenjun He, Zhimeng Xu, Yanqing Li, Yanan Yang, Zhaowei Huang, Panjing Lv, Xin Wang, Dali Han, Yan Li, Nan Qiao, Bing Liu
:
Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server. 5735-5745 - Sorin I. Avram
, Ramona Curpan, Liliana Halip
, Alina Bora, Tudor I. Oprea
:
Off-Patent Drug Repositioning. 5746-5753 - Sumit Kumar, Prem Prakash Sharma, Uma Shankar
, Dhruva Kumar, Sanjeev K. Joshi, Lindomar Pena, Ravi Durvasula, Amit Kumar, Prakasha Kempaiah, Poonam
, Brijesh Rathi
:
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure-Activity Relationship Studies. 5754-5770 - Son Tung Ngo
, Ngoc Quynh Anh Pham, Ly Thi Le, Duc-Hung Pham, Van V. Vu
:
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. 5771-5780 - Anuj Gahlawat
, Navneet Kumar
, Rajender Kumar
, Hardeep Sandhu, Inder Pal Singh, Saranjit Singh
, Anders Sjöstedt
, Prabha Garg
:
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease. 5781-5793 - Junjie Zou, Jian Yin
, Lei Fang, Mingjun Yang, Tianyuan Wang, Weikun Wu, Michael A. Bellucci, Peiyu Zhang:
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations. 5794-5802 - Helen M. Deeks, Rebecca Walters
, Jonathan Barnoud
, David R. Glowacki
, Adrian J. Mulholland
:
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. 5803-5814 - Dimas Suárez
, Natalia Díaz
:
SARS-CoV-2 Main Protease: A Molecular Dynamics Study. 5815-5831 - Atanu Acharya
, Rupesh Agarwal
, Matthew B. Baker, Jérôme Baudry
, Debsindhu Bhowmik
, Swen Böhm, Kendall G. Byler, Sam Yen-Chi Chen, Leighton Coates
, Connor J. Cooper
, Omar Demerdash, Isabella Daidone
, John D. Eblen, Sally R. Ellingson, Stefano Forli
, Jens Glaser
, James C. Gumbart
, John Gunnels, Oscar R. Hernandez, Stephan Irle
, Daniel W. Kneller
, Andrey Kovalevsky
, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu
, Julie C. Mitchell, Gilchan Park, Jerry M. Parks
, Anna Pavlova, Loukas Petridis
, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers
, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova
, Yue Shen, Jeremy C. Smith
, Micholas Dean Smith
, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas
, Van Quan Vuong
, Junqi Yin, Shinjae Yoo
, Mai Zahran, Laura Zanetti Polzi
:
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. 5832-5852 - Rui Wang
, Yuta Hozumi
, Changchuan Yin
, Guo-Wei Wei
:
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. 5853-5865 - Ariane Nunes-Alves
, Angelica Mazzolari
, Kenneth M. Merz Jr.
:
What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling. 5866-5867 - Kenneth M. Merz Jr.
, Rommie E. Amaro
, Zoe Cournia
, Matthias Rarey
, Thereza A. Soares
, Alexander Tropsha
, Habibah A. Wahab
, Renxiao Wang
:
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. 5868-5869 - Wenxi Zhao, Dmitriy Korobskiy
, Shreya Chandrasekharan
, Kenneth M. Merz Jr.
, George Chacko
:
Converging Interests: Chemoinformatics, History, and Bibliometrics. 5870-5872 - Gerald M. Maggiora, José L. Medina-Franco
, Javed Iqbal, Martin Vogt
, Jürgen Bajorath
:
From Qualitative to Quantitative Analysis of Activity and Property Landscapes. 5873-5880 - Felipe Rodrigues Souza
, Lucas Miguel Pereira Souza
, André Silva Pimentel
:
Recent Open Issues in Coarse Grained Force Fields. 5881-5884 - Igor Barden Grillo, Gabriel Aires Urquiza-Carvalho
, Gerd Bruno Rocha
:
PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules. 5885-5890 - Maho Nakata
, Tomomi Shimazaki
, Masatomo Hashimoto
, Toshiyuki Maeda
:
PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties. 5891-5899 - Jinwen Shan, Xiaolin Pan
, Xingyu Wang, Xudong Xiao, Changge Ji
:
FragRep: A Web Server for Structure-Based Drug Design by Fragment Replacement. 5900-5906 - Piotr Setny
:
GridSolvate: A Web Server for the Prediction of Biomolecular Hydration Properties. 5907-5911 - Lotfi Boudjema, Hanna Aarrass, Marwa Assaf, Marie Morille
, Gaelle Martin-Gassin
, Pierre-Marie Gassin
:
PySHS: Python Open Source Software for Second Harmonic Scattering. 5912-5917 - Thomas Blaschke, Josep Arús-Pous, Hongming Chen, Christian Margreitter
, Christian Tyrchan
, Ola Engkvist
, Kostas Papadopoulos
, Atanas Patronov
:
REINVENT 2.0: An AI Tool for De Novo Drug Design. 5918-5922 - Victor H. Rusu, Denys E. S. Santos
, Marcelo Depólo Polêto
, Marcelo Galheigo, Antônio Tadeu A. Gomes, Hugo Verli
, Thereza A. Soares
, Roberto D. Lins
:
Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. 5923-5927 - Malte Döntgen
, Yann Fenard
, K. Alexander Heufer:
Atomic Partial Charges as Descriptors for Barrier Heights. 5928-5931 - Yaozong Li
, Rajiv K. Bedi, Elena V. Moroz-Omori
, Amedeo Caflisch
:
Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. 5932-5935 - Doyeong Hwang, Soojung Yang, Yongchan Kwon, Kyung-Hoon Lee, Grace Lee, Hanseok Jo, Seyeol Yoon, Seongok Ryu
:
Comprehensive Study on Molecular Supervised Learning with Graph Neural Networks. 5936-5945 - Nurlybek Amangeldiuly
, Dmitry Karlov
, Maxim V. Fedorov:
Baseline Model for Predicting Protein-Ligand Unbinding Kinetics through Machine Learning. 5946-5956 - Elena L. Cáceres
, Nicholas C. Mew, Michael J. Keiser
:
Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction. 5957-5970 - Obaidur Rahaman
, Alessio Gagliardi
:
Deep Learning Total Energies and Orbital Energies of Large Organic Molecules Using Hybridization of Molecular Fingerprints. 5971-5983 - Beomchang Kang
, Chaok Seok
, Juyong Lee
:
Prediction of Molecular Electronic Transitions Using Random Forests. 5984-5994 - Pracheta Sahoo, Indranil Roy
, Zhuoyi Wang, Feng Mi, Lin Yu, Pradeep Balasubramani, Latifur Khan
, J. Fraser Stoddart
:
MultiCon: A Semi-Supervised Approach for Predicting Drug Function from Chemical Structure Analysis. 5995-6006 - Vishal B. Siramshetty
, Dac-Trung Nguyen, Natalia J. Martinez, Noel Southall
, Anton Simeonov, Alexey V. Zakharov
:
Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the "Big Data" Era. 6007-6019 - Dragos Horvath
, Gilles Marcou
, Alexandre Varnek
:
Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control. 6020-6032 - Gerardo Valadez Huerta
, Gabriele Raabe
:
Genetic Parameterization of Interfacial Force Fields Based on Classical Bulk Force Fields and Ab Initio Data: Application to the Methanol-ZnO Interfaces. 6033-6043 - Maximilian Grimm, Yang Liu
, Xiaocong Yang, Chunya Bu, Zhixiong Xiao, Yang Cao
:
LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. 6044-6053 - Sheng Gui
, Zhaodi Chen, Benzhuo Lu
, Minxin Chen:
Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization. 6054-6064 - John J. Irwin
, Khanh G. Tang, Jennifer Young, Chinzorig Dandarchuluun, Benjamin R. Wong, Munkhzul Khurelbaatar, Yurii S. Moroz, John W. Mayfield
, Roger A. Sayle:
ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand Discovery. 6065-6073 - Pavel G. Polishchuk
:
Control of Synthetic Feasibility of Compounds Generated with CReM. 6074-6080 - Dominique Sydow
, Paula Schmiel
, Jérémie Mortier
, Andrea Volkamer
:
KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. 6081-6094 - Jacqueline M. Cole
:
Enumerating Intramolecular Charge Transfer in Conjugated Organic Compounds. 6095-6108 - Ekaterina Elts
, Heiko Briesen
:
Capturing Crystal Shape Evolution from Molecular Simulations. 6109-6119 - Hans Matter
, Christian Buning, Dan Dragos Stefanescu, Sven Ruf, Gerhard Hessler:
Using Graph Databases to Investigate Trends in Structure-Activity Relationship Networks. 6120-6134 - David Balcells
, Bastian Bjerkem Skjelstad
:
tmQM Dataset - Quantum Geometries and Properties of 86k Transition Metal Complexes. 6135-6146 - Donald Loveland, Bhavya Kailkhura, Piyush Karande
, Anna M. Hiszpanski
, Thomas Yong-Jin Han
:
Automated Identification of Molecular Crystals' Packing Motifs. 6147-6154 - Sebastian Mosbach
, Angiras Menon, Feroz Farazi
, Nenad B. Krdzavac, Xiaochi Zhou, Jethro Akroyd
, Markus Kraft
:
Multiscale Cross-Domain Thermochemical Knowledge-Graph. 6155-6166 - Chun Jiang Zhu
, Minghu Song
, Qinqing Liu, Chloé Becquey, Jinbo Bi:
Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search. 6167-6184 - Leila Tabrizi
, Thi Le Anh Nguyen
, Hoang Dieu Thao Tran, Minh Quan Pham
, Duy Quang Dao
:
Antioxidant and Anticancer Properties of Functionalized Ferrocene with Hydroxycinnamate Derivatives - An Integrated Experimental and Theoretical Study. 6185-6203 - Felipe J. Valencia
, Max Ramírez
, Alejandro Varas, José Rogan
, Miguel Kiwi
:
Thermal Stability of Hollow Porous Gold Nanoparticles: A Molecular Dynamics Study. 6204-6210 - Steven K. Albanese
, John D. Chodera
, Andrea Volkamer
, Simon Keng, Robert Abel, Lingle Wang
:
Is Structure-Based Drug Design Ready for Selectivity Optimization? 6211-6227 - Gabriela L. Borosky
:
Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein. 6228-6241 - Amina Abula, Zhijian Xu
, Zhengdan Zhu
, Cheng Peng, Zhaoqiang Chen, Weiliang Zhu
, Haji Akber Aisa
:
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. 6242-6250 - Jamie R. Nuñez, Monee Y. McGrady, Yasemin Yesiltepe, Ryan S. Renslow
, Thomas O. Metz
:
Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets. 6251-6257 - Shae-Lynn J. Lahey, Tu Nguyen Thien Phuc, Christopher N. Rowley
:
Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments. 6258-6268 - Patrick Penner
, Virginie Y. Martiny, Arnaud Gohier, Marcus Gastreich, Pierre Ducrot, David Brown, Matthias Rarey
:
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. 6269-6281 - Felipe Curtolo
, Guilherme Menegon Arantes
:
Mechanisms for Flavin-Mediated Oxidation: Hydride or Hydrogen-Atom Transfer? 6282-6287 - Maria G. Khrenova
, Fedor D. Mulashkin
, Egor S. Bulavko, Tatiana M. Zakharova, Alexander V. Nemukhin
:
Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores. 6288-6297 - Atilio Reyes Romero, Angel Jonathan Ruiz-Moreno
, Matthew R. Groves
, Marco Velasco-Velázquez
, Alexander S. Dömling
:
Benchmark of Generic Shapes for Macrocycles. 6298-6313 - Haochen Xie
, Saurabh Basu, Edward C. DeMeter:
Molecular Dynamics Simulations of Photo-Induced Free Radical Polymerization. 6314-6327 - Eric D. Boittier
, Jed M. Burns, Neha Gandhi
, Vito Ferro
:
GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans. 6328-6343 - Jordi Juárez Jiménez
, Philip Tew, Michael O'Connor, Salomé Llabrés
, Rebecca Sage, David R. Glowacki
, Julien Michel
:
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes. 6344-6354 - Jingxiao Bao, Xiao He
, John Z. H. Zhang
:
Development of a New Scoring Function for Virtual Screening: APBScore. 6355-6365 - Akshay Prabhakant, Abhinandan Panigrahi, Marimuthu Krishnan
:
Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding. 6366-6376 - Gauri Thapa, Akash Bhattacharya, Swati Bhattacharya
:
Dimeric Hold States of Anti-HIV Protein SAMHD1 are Redox Tunable. 6377-6391 - Wayde Veldman
, Marcelo Vizona Liberato, Vitor M. Almeida
, Valquiria P. Souza, Maira A. Frutuoso, Sandro R. Marana
, Vuyani Moses, Özlem Tastan Bishop
, Igor Polikarpov
:
X-ray Structure, Bioinformatics Analysis, and Substrate Specificity of a 6-Phospho-β-glucosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis. 6392-6407 - Isaac de Araújo Matos
, Nivan Bezerra da Costa Júnior
, Flavia Carla Meotti
:
Integration of an Inhibitor-like Rule and Structure-based Virtual Screening for the Discovery of Novel Myeloperoxidase Inhibitors. 6408-6418 - Tod D. Romo, Alan Grossfield
, Andrea G. Markelz
:
Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis. 6419-6426 - Aakash Saha
, Pablo R. Arantes
, Rohaine V. Hsu, Yogesh B. Narkhede
, Martin Jinek, Giulia Palermo
:
Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. 6427-6437 - Shaima Hashem
, William George Davies, Arianna Fornili
:
Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin. 6438-6446 - Ozge Kurkcuoglu
, M. Unal Gunes, Turkan Haliloglu:
Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome. 6447-6461 - Suman Samantray
, Feng Yin, Batuhan Kav
, Birgit Strodel
:
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. 6462-6475 - Brian D. Ratnasinghe
, Alexa M. Salsbury
, Justin A. Lemkul
:
Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field. 6476-6488 - Mahdi Mousaei, Meruyert Kudaibergenova, Alexander D. MacKerell Jr.
, Sergei Yu Noskov
:
Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. 6489-6501 - Florian Flachsenberg
, Agnes Meyder
, Kai Sommer
, Patrick Penner
, Matthias Rarey
:
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. 6502-6522 - Adolfo Bastida
, Jose Zuñiga, Alberto Requena
, Beatriz Miguel, Javier Cerezo
:
On the Role of Entropy in the Stabilization of α-Helices. 6523-6531 - Riccardo Ocello, Simone Furini
, Francesca Lugli
, Maurizio Recanatini
, Carmen Domene
, Matteo Masetti
:
Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields. 6532-6543 - Laura Chachulski
, Björn Windshügel
:
LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance. 6544-6554 - Alice Ballone, Francesca Picarazzi
, Christine Prosser, Jeremy Davis
, Christian Ottmann
, Mattia Mori
:
Experimental and Computational Druggability Exploration of the 14-3-3ζ/SOS1pS1161 PPI Interface. 6555-6565 - Holly Freedman
, Juthika Kundu, Egor Petrovitch Tchesnokov, John Lok Man Law, James A. Nieman
, Raymond F. Schinazi
, D. Lorne Tyrrell, Matthias Gotte
, Michael Houghton
:
Application of Molecular Dynamics Simulations to the Design of Nucleotide Inhibitors Binding to Norovirus Polymerase. 6566-6578 - Levente M. Mihalovits
, György G. Ferenczy
, György M. Keserü
:
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations. 6579-6594 - Andreas Tosstorff
, Jason C. Cole
, Robin Taylor
, Seth F. Harris, Bernd Kuhn
:
Identification of Noncompetitive Protein-Ligand Interactions for Structural Optimization. 6595-6611 - Amanda E. Wakefield
, Christine Yueh, Dmitri Beglov, Marcelo Santos Castilho
, Dima Kozakov
, György M. Keserü
, Adrian Whitty
, Sandor Vajda
:
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. 6612-6623 - Dongxiao Hao
, Xibing He
, Beihong Ji
, Shengli Zhang
, Junmei Wang
:
How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations? 6624-6633 - Pilar A. Vásquez, Loreto San Martín, Yenifer Argel, Camila Riquelme, Josefa Torres, Felipe Vidal, Francisca Cayuman, Patricio Castro
, Jorge Fuentealba, Gustavo Moraga-Cid
, Gonzalo Yevenes
, Chunyang Jin
, Verónica A. Jiménez
, Leonardo Guzmán
:
Stereospecific Inhibition of Ethanol Potentiation on Glycine Receptor by M554 Stereoisomers. 6634-6641 - Charleen G. Don
, Martin Smiesko
:
Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations. 6642-6653 - Tobias Hüfner-Wulsdorf
, Gerhard Klebe
:
Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms. 6654-6665 - Phasit Charoenkwan, Janchai Yana
, Chanin Nantasenamat
, Md. Mehedi Hasan
, Watshara Shoombuatong
:
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides. 6666-6678 - Anupam Banerjee
, Amit Kumar, Kushal Kanti Ghosh
, Pralay Mitra
:
Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures. 6679-6690 - Gang Xu, Qinghua Wang, Jianpeng Ma
:
OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods. 6691-6697 - Yuyu Feng, Sheng-You Huang
:
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid-Ligand Interactions. 6698-6708 - Cong Shen
, Jiawei Luo, Wenjue Ouyang, Pingjian Ding
, Hao Wu:
Identification of Small Molecule-miRNA Associations with Graph Regularization Techniques in Heterogeneous Networks. 6709-6721 - Ulf Norinder, Ola Spjuth
, Fredrik Svensson
:
Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling". 6722
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