default search action
Journal of Chemical Information and Modeling, Volume 60
Volume 60, Number 1, January 2020
- Kira A. Armacost
, Sereina Riniker
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
GRAM: A True Null Model for Relative Binding Affinity Predictions. 11-16 - Congcong Gong
New Discoveries in Hybrid Orbitals to Characterize Molecules and Predict Biomolecular Interactions. 17-21 - Vadim Korolev
Graph Convolutional Neural Networks as "General-Purpose" Property Predictors: The Universality and Limits of Applicability. 22-28 - Seung Hwan Hong
Molecular Generative Model Based on an Adversarially Regularized Autoencoder. 29-36 - Pingjian Ding
Incorporating Multisource Knowledge To Predict Drug Synergy Based on Graph Co-regularization. 37-46 - Shuangjia Zheng
Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. 47-55 - Vikram Sundar
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
Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. 63-76 - Yibo Li
DeepScaffold: A Comprehensive Tool for Scaffold-Based De Novo Drug Discovery Using Deep Learning. 77-91 - Yan Yang, Yanmin Zhang
In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality. 92-107 - Feroz Farazi
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
Building Highly Reliable Quantitative Structure-Activity Relationship Classification Models Using the Rivality Index Neighborhood Algorithm with Feature Selection. 133-151 - Tigran M. Abramyan
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
Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. 175-191 - Callum J. Dickson
Revealing Molecular Determinants of hERG Blocker and Activator Binding. 192-203 - Nguyen Thanh Nguyen, Trung Hai Nguyen
Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. 204-211 - Rabindranath Paul
Computational Study of Encapsulation of Polyaromatic Hydrocarbons by Endo-Functionalized Receptors in Nonpolar Medium. 212-225 - Pharit Kamsri
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
Benchmarking Electronic Structure Methods for Accurate Fixed-Charge Electrostatic Models. 249-258 - Mark A. J. Koenis, Olivier Visser, Lucas Visscher
GUI Implementation of VCDtools, A Program to Analyze Computed Vibrational Circular Dichroism Spectra. 259-267 - Miguel Ponce-Vargas
Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host-Guest Assemblies. 268-278 - Matthias Diem
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. 279-288 - Joseph M. Jakubowski, Asuka A. Orr
Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations. 289-305 - Zhenlu Li
Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface. 306-315 - Quan Van Vo
In Silico Study of the Radical Scavenging Activities of Natural Indole-3-Carbinols. 316-321 - Leandro Oliveira Bortot
Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. 322-331 - Maninder Singh
Computational Design of Biologically Active Anticancer Peptides and Their Interactions with Heterogeneous POPC/POPS Lipid Membranes. 332-341 - Abdennour Braka, Norbert Garnier
Residence Time Prediction of Type 1 and 2 Kinase Inhibitors from Unbinding Simulations. 342-348 - Maywan Hariono
Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling. 349-359 - Eva-Maria Zangerl-Plessl
Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574. 360-371 - Luca Pinzi
Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank. 372-390 - Sheng Chen
To Improve Protein Sequence Profile Prediction through Image Captioning on Pairwise Residue Distance Map. 391-399 - Cong Fan
DStruBTarget: Integrating Binding Affinity with Structure Similarity for Ligand-Binding Protein Prediction. 400-409 - Xiaoqiang Huang
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. 410-420 - Neeraj Kumar
Multiepitope Subunit Vaccine to Evoke Immune Response against Acute Encephalitis. 421-433
Volume 60, Number 2, February 2020
- Thereza A. Soares
Outlook on the Development and Application of Molecular Simulations in Latin America. 435-438 - Lucas A. Silva
GEMS-Pack: A Graphical User Interface for the Packmol Program. 439-443 - Roy González-Alemán
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
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
Quality Threshold Clustering of Molecular Dynamics: A Word of Caution. 467-472 - Denys E. S. Santos
SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. 473-484 - Rafael Maglia de Souza
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
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
Are the Absorption Spectra of Doxorubicin Properly Described by Considering Different Tautomers? 513-521 - Rafael Maglia de Souza
Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles. 522-536 - Krys E. A. Batista
Ab Initio Investigation of CO2 Adsorption on 13-Atom 4d Clusters. 537-545 - Paulo Henrique Borges Ferreira
The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins. 546-561 - Felipe R. S. Santos
Identification of a Potential Zika Virus Inhibitor Targeting NS5 Methyltransferase Using Virtual Screening and Molecular Dynamics Simulations. 562-568 - Franccesca Fornasier
Lipophilicity of Coarse-Grained Cholesterol Models. 569-577 - Igor Barden Grillo, Gabriel Aires Urquiza-Carvalho
Elucidating Enzymatic Catalysis Using Fast Quantum Chemical Descriptors. 578-591 - Fiorella Cravero
Feature Selection for Polymer Informatics: Evaluating Scalability and Robustness of the FS4RVDD Algorithm Using Synthetic Polydisperse Data Sets. 592-603 - Laura Mortara, Hernan Chaimovich
Dehydration Determines Hydrotropic Ion Affinity for Zwitterionic Micelles. 604-610 - Fernando Alvarez-Ramírez
Database of Nuclear Independent Chemical Shifts (NICS) versus NICSZZ of Polycyclic Aromatic Hydrocarbons (PAHs). 611-620 - Lucas G. Viviani
Virtual Screening Approach for the Identification of Hydroxamic Acids as Novel Human Ecto-5′-Nucleotidase Inhibitors. 621-630 - Pablo R. Arantes
The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains. 631-643 - Yaicel G. Proenza
Simulation of the Adsorption and Release of Large Drugs by ZIF-8. 644-652 - Murilo H. Teixeira
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
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
Current Status of Carbohydrates Information in the Protein Data Bank. 684-699 - Sarah Arvelos
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
Modeling the Field Emission Enhancement Factor for Capped Carbon Nanotubes Using the Induced Electron Density. 714-721 - Juan I. Melo
Performance of the LRESC Model on top of DFT Functionals for Relativistic NMR Shielding Calculations. 722-730 - Felipe R. S. Santos
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
Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. 738-746 - Alvaro J. Lopez
On the Interpretation of subtilisin Carlsberg Time-Resolved Fluorescence Anisotropy Decays: Modeling with Classical Simulations. 747-755 - Giacomo Rossino
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
Insight into the Interaction Mechanism of Nicotine, NNK, and NNN with Cytochrome P450 2A13 Based on Molecular Dynamics Simulation. 766-776 - Rodrigo Aguayo-Ortiz
Effects of Mutating Trp42 Residue on γD-Crystallin Stability. 777-785 - Brianda L. Santini, Matías Zúñiga-Bustos
In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy. 786-793 - N. R. Carina Alves
Structural Insights into the Ligand Binding Domain of the Glucocorticoid Receptor: A Molecular Dynamics Study. 794-804 - Antistio Alviz-Amador
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
Kinase Activation by Small Conformational Changes. 821-832 - Federico A. Olivieri
Conformational and Reaction Dynamic Coupling in Histidine Kinases: Insights from Hybrid QM/MM Simulations. 833-842 - Jonathan Alexis Semelak
Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. 843-853 - Cecilia Prudkin-Silva
Combined Experimental and Molecular Simulation Study of Insulin-Chitosan Complexation Driven by Electrostatic Interactions. 854-865 - Ángel Santiago
Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. 866-879 - Clauber Henrique Costa
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
Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation-π Contacts in Proteins. 890-897 - Jocelyn Solorza
Molecular Insights into the Trapping Effect of Ca2+ in Protein Kinase A: A Molecular Dynamics Study. 898-914 - Fernanda Mendoza
Catalytic Role of Gln202 in the Carboligation Reaction Mechanism of Yeast AHAS: A QM/MM Study. 915-922 - Vanesa Racigh, Agustín Ormazábal
Positively Charged Residues in the Head Domain of P2X4 Receptors Assist the Binding of ATP. 923-932 - Fernanda Mendoza
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
Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. 944-963 - Pablo G. Garay
Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field. 964-973 - Matías Martínez, Christopher D. Cooper
Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. 974-981 - Fernando Bruno da Silva
Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. 982-988 - Simón Poblete
Brief Comparison between Experimental and Computationally Generated Ensembles of RNA Dinucleotides. 989-994 - Pilar A. Vásquez, Felipe Vidal, Josefa Torres, Verónica A. Jiménez
Rational Design and In Vitro Evaluation of Novel Peptides Binding to Neuroligin-1 for Synaptic Targeting. 995-1004 - José X. Lima Neto
Exploring the Binding Mechanism of GABAB Receptor Agonists and Antagonists through in Silico Simulations. 1005-1018 - Natali Acosta-Tapia
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
Discovery of Potent, Reversible, and Competitive Cruzain Inhibitors with Trypanocidal Activity: A Structure-Based Drug Design Approach. 1028-1041 - Ernesto Contreras-Torres
MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. 1042-1059 - Marcelo Querino Lima Afonso
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.
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
libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. 1079-1084 - Oya Wahl
Tautobase: An Open Tautomer Database. 1085-1089 - Devendra K. Dhaked
Tautomer Database: A Comprehensive Resource for Tautomerism Analyses. 1090-1100 - Thanh-Hoang Nguyen-Vo
Plant Metabolite Databases: From Herbal Medicines to Modern Drug Discovery. 1101-1110 - Ece Asilar
Image Based Liver Toxicity Prediction. 1111-1121 - Minyi Su
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
Costless Performance Improvement in Machine Learning for Graph-Based Molecular Analysis. 1137-1145 - Na Le Dang
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors. 1146-1164 - Shimin Su
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
Bidirectional Molecule Generation with Recurrent Neural Networks. 1175-1183 - Yunqi Shao
PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials. 1184-1193 - Edward Kim
Inorganic Materials Synthesis Planning with Literature-Trained Neural Networks. 1194-1201 - Jie Xia
Pose Filter-Based Ensemble Learning Enables Discovery of Orally Active, Nonsteroidal Farnesoid X Receptor Agonists. 1202-1214 - Cecile Valsecchi
Consensus versus Individual QSARs in Classification: Comparison on a Large-Scale Case Study. 1215-1223 - G. C. Loh
Viscosity Prediction of Lubricants by a General Feed-Forward Neural Network. 1224-1234 - Jian Jiang, Rui Wang
Boosting Tree-Assisted Multitask Deep Learning for Small Scientific Datasets. 1235-1244 - Yifei Qi
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet. 1245-1252 - Devendra K. Dhaked
Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. 1253-1275 - Philip V. Toukach
New Features of Carbohydrate Structure Database Notation (CSDB Linear), As Compared to Other Carbohydrate Notations. 1276-1289 - Joshua Kammeraad
What Does the Machine Learn? Knowledge Representations of Chemical Reactivity. 1290-1301 - Oleksandr Kravchenko
A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction. 1302-1316 - Enrico Margiotta
Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design. 1317-1328 - Duy Quang Dao
Insight into Antioxidant and Photoprotective Properties of Natural Compounds from Marine Fungus. 1329-1351 - Maria Cecilia Barrera
A Polarization-Consistent Model for Alcohols to Predict Solvation Free Energies. 1352-1367 - Sébastien Dilly
In Silico Identification of a Key Residue for Substrate Recognition of the Riboflavin Membrane Transporter RFVT3. 1368-1375 - Hideaki Takahashi
Large-Scale Parallel Implementation of Hartree-Fock Exchange Energy on Real-Space Grids Using 3D-Parallel Fast Fourier Transform. 1376-1389 - Lorenzo Di Rienzo
Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors. 1390-1398 - Huynh Minh Hung
Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide. 1399-1408 - Tobias Hüfner-Wulsdorf
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals. 1409-1423 - Shi Li, Balaji Sesha Sarath Pokuri
Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach. 1424-1431 - Daniel Cappel
Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. 1432-1444 - Jacinto Sandoval-Lira, Gustavo Mondragón-Solórzano
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
Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design. 1453-1460 - Julian Zachmann, Eftichia Kritsi
Combined Computational and Structural Approach into Understanding the Role of Peptide Binding and Activation of Melanocortin Receptor 4. 1461-1468 - Silvia Rinaldi
Mechanistic Model for the Hsp90-Driven Opening of Human Argonaute. 1469-1480 - Laura Pedraza-González
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
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. 1509-1527 - Lucia Fusani, David S. Palmer
Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. 1528-1539 - Yue Chen, Junhao Li, Zengrui Wu, Guixia Liu
Computational Insight into the Allosteric Activation Mechanism of Farnesoid X Receptor. 1540-1550 - Rongfeng Zou
Free Energy Profile and Kinetics of Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2. 1551-1558 - Vladimír Sládek
Protein Dynamics and the Folding Degree. 1559-1567 - Christina Nutschel, Alexander Fulton, Olav Zimmermann, Ulrich Schwaneberg
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
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
Molecular Determinants for the Activation/Inhibition of Bak Protein by BH3 Peptides. 1632-1643 - Maciej Majewski
Structural Stability Predicts the Binding Mode of Protein-Ligand Complexes. 1644-1651 - Hristina R. Zhekova
Mapping of Ion and Substrate Binding Sites in Human Sodium Iodide Symporter (hNIS). 1652-1665 - José Rogério A. Silva
Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism. 1666-1677 - Dinesh Kumar Sriramulu
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
Druggability Assessment in TRAPP Using Machine Learning Approaches. 1685-1699 - Chaoqun Li
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
Methodology for Further Thermostabilization of an Intrinsically Thermostable Membrane Protein Using Amino Acid Mutations with Its Original Function Being Retained. 1709-1716 - Liang Dai
Discovery of Novel Peroxisome Proliferator-Activated Receptor α (PPARα) Agonists by Virtual Screening and Biological Evaluation. 1717-1727 - Carles Perez
FragPELE: Dynamic Ligand Growing within a Binding Site. A Novel Tool for Hit-To-Lead Drug Design. 1728-1736 - Abdurrahman Olgaç
Discovery of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by Exploiting a Multistep Virtual Screening Protocol. 1737-1748 - Holli-Joi Sullivan
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
Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors. 1766-1778 - Julio Gomis-Tena
When Does the IC50 Accurately Assess the Blocking Potency of a Drug? 1779-1790 - Nasim Ahmadian, Faramarz Mehrnejad
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
A Supervised Molecular Dynamics Approach to Unbiased Ligand-Protein Unbinding. 1804-1817 - Tobias Hüfner-Wulsdorf
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
Exploration and Evaluation of Machine Learning-Based Models for Predicting Enzymatic Reactions. 1833-1843 - Agnieszka S. Karczynska
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. 1844-1864 - Jiansheng Wu
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
Simulated Epidemics in 3D Protein Structures to Detect Functional Properties. 1884-1891 - Ayisha Zia
In Silico Exploration of Conformational Dynamics and Novel Inhibitors for Targeting MEF2-Associated Transcriptional Activity. 1892-1909 - Robert P. Sheridan
Correction to Extreme Gradient Boosting as a Method for Quantitative Structure-Activity Relationships. 1910
Volume 60, Number 4, April 2020
- Peter R. Curran
Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design. 1911-1916 - Miroslav Suruzhon
ProtoCaller: Robust Automation of Binding Free Energy Calculations. 1917-1921 - Gudrun Gygli
Simulation Foundry: Automated and F.A.I.R. Molecular Modeling. 1922-1927 - Balaranjan Selvaratnam
Application of Symmetry Functions to Large Chemical Spaces Using a Convolutional Neural Network. 1928-1935 - James Houston, Frank G. Glavin
Robust Classification of High-Dimensional Spectroscopy Data Using Deep Learning and Data Synthesis. 1936-1954 - Amanda J. Minnich
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery. 1955-1968 - Robert P. Sheridan
Experimental Error, Kurtosis, Activity Cliffs, and Methodology: What Limits the Predictivity of Quantitative Structure-Activity Relationship Models? 1969-1982 - Fergus Imrie
Deep Generative Models for 3D Linker Design. 1983-1995 - Juhwan Noh
Uncertainty-Quantified Hybrid Machine Learning/Density Functional Theory High Throughput Screening Method for Crystals. 1996-2003 - Hong Wang, Yunchao Xie
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
A New Machine-Learning Tool for Fast Estimation of Liquid Viscosity. Application to Cosmetic Oils. 2012-2023 - Youngchun Kwon, Dongseon Lee, Youn-Suk Choi
Neural Message Passing for NMR Chemical Shift Prediction. 2024-2030 - Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou
Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. 2031-2043 - Shuzhe Wang
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. 2044-2058 - Edward J. Beard
ChemSchematicResolver: A Toolkit to Decode 2D Chemical Diagrams with Labels and R-Groups into Annotated Chemical Named Entities. 2059-2072 - Hiroshi Nakano
Exploring Topological Pharmacophore Graphs for Scaffold Hopping. 2073-2081 - Tao Zeng
TeroKit: A Database-Driven Web Server for Terpenome Research. 2082-2090 - Michael J. Bower
Smallest Maximum Intramolecular Distance: A Novel Method to Mitigate Pregnane Xenobiotic Receptor Activation. 2091-2099 - Jade Simões de Castro
In Silico Infrared Characterization of Synthetic Cannabinoids by Quantum Chemistry and Chemometrics. 2100-2114 - Juan José Gamboa-Carballo
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
TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations. 2126-2137 - Erick López-Chávez, Gerardo Pérez-Hernández
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
Self-Assembled Two-Dimensional Nanoporous Crystals as Molecular Sieves: Molecular Dynamics Studies of 1, 3, 5-Tristyrilbenzene-Cn Superstructures. 2155-2168 - Rohit Goswami
d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations. 2169-2177 - Philipp S. Schmalhorst
A Grid Map Based Approach to Identify Nonobvious Ligand Design Opportunities in 3D Protein Structure Ensembles. 2178-2188 - Hugo Guterres
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. 2189-2198 - Qiyuan Zhao
Self-Consistent Component Increment Theory for Predicting Enthalpy of Formation. 2199-2207 - Zheng Wan, Guobing Zhou
Separation Selectivity of CH4/CO2 Gas Mixtures in the ZIF-8 Membrane Explored by Dynamic Monte Carlo Simulations. 2208-2218 - Rao Huang
Basin Hopping Genetic Algorithm for Global Optimization of PtCo Clusters. 2219-2228 - Arghya Chakravorty
Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. 2229-2246 - Krzysztof K. Bojarski
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study. 2247-2256 - Dong Song
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. 2257-2267 - Laust Moesgaard
Modeling the Sterol-Binding Domain of Aster-A Provides Insight into Its Multiligand Specificity. 2268-2281 - Christopher Lockhart
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
Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. 2294-2303 - Johannes R. Loeffler
STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. 2304-2313 - Gerard Martínez-Rosell
PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. 2314-2324 - Alena Randáková
Agonist-Specific Conformations of the M2 Muscarinic Acetylcholine Receptor Assessed by Molecular Dynamics. 2325-2338 - Robert G. Brinson
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
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
Accurately Predicting Mutation-Caused Stability Changes from Protein Sequences Using Extreme Gradient Boosting. 2388-2395 - Sugunadevi Sakkiah, Carmine Leggett, Bohu Pan, Wenjing Guo
Development of a Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model. 2396-2404 - Panagiotis Lagarias, Kerry Barkan, Eva Tzortzini
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
Faces of Contemporary CryoEM Information and Modeling. 2407-2409 - James S. Fraser
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
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
Structural Biology in the Multi-Omics Era. 2424-2429 - Liam J. Worrall
Aligning the Symmetry of the Type III Secretion System Needle Complex. 2430-2435 - Doo Nam Kim
Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. 2436-2442 - Luciano A. Abriata
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
What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. 2458-2469 - Thomas Dodd
Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy. 2470-2483 - Suvrajit Maji
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
ImageDataExtractor: A Tool To Extract and Quantify Data from Microscopy Images. 2492-2509 - Jure Borisek
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
Integration of Cryo-EM Model Building Software in Scipion. 2533-2540 - Carlos F. Rodríguez
Modeling of a 14 kDa RUVBL2-Binding Domain with Medium Resolution Cryo-EM Density. 2541-2551 - Agnel Praveen Joseph
Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit Using Difference Maps. 2552-2560 - Andreas D. Schenk
Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE. 2561-2569 - Sandhya P. Tiwari
Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps. 2570-2580 - Evan Seitz
POLARIS: Path of Least Action Analysis on Energy Landscapes. 2581-2590 - John W. Vant, Shae-Lynn J. Lahey, Kalyanashis Jana
Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials. 2591-2604 - Yue Zhang
Could Egg White Lysozyme be Solved by Single Particle Cryo-EM? 2605-2613 - Rui Xie, Yu-Xuan Chen
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
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
Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps. 2644-2650
Volume 60, Number 6, June 2020
- Cynthia J. Burrows
Update to Our Reader, Reviewer, and Author Communities - April 2020. 2651-2652 - Rommie E. Amaro
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
ADME Prediction with KNIME: Development and Validation of a Publicly Available Workflow for the Prediction of Human Oral Bioavailability. 2660-2667 - Federico Lazzari
Molecular Perception for Visualization and Computation: The Proxima Library. 2668-2672 - Alejandro Varela-Rial
SkeleDock: A Web Application for Scaffold Docking in PlayMolecule. 2673-2677 - Remco Hens, Ahmadreza Rahbari
Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method. 2678-2682 - Zhengdan Zhu
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. 2683-2696 - Gabriele Scalia
Evaluating Scalable Uncertainty Estimation Methods for Deep Learning-Based Molecular Property Prediction. 2697-2717 - Dimitri Panagopoulos Abrahamsson
Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards. 2718-2727 - Christos A. Nicolaou
Context Aware Data-Driven Retrosynthetic Analysis. 2728-2738 - Weikaixin Kong
Prediction and Optimization of NaV1.7 Sodium Channel Inhibitors Based on Machine Learning and Simulated Annealing. 2739-2753 - Yanxing Wang
TF3P: Three-Dimensional Force Fields Fingerprint Learned by Deep Capsular Network. 2754-2765 - Fangqiang Zhu
Binding Affinity Prediction by Pairwise Function Based on Neural Network. 2766-2772 - Yuting Xu
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
Coarse-Grained Diffraction Template Matching Model to Retrieve Multiconformational Models for Biomolecule Structures from Noisy Diffraction Patterns. 2803-2818 - María Gálvez-Llompart
Identification of New Templates for the Synthesis of BEA, BEC, and ISV Zeolites Using Molecular Topology and Monte Carlo Techniques. 2819-2829 - Ulf Norinder
Using Predicted Bioactivity Profiles to Improve Predictive Modeling. 2830-2837 - Rachael A. Mansbach
Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. 2838-2847 - Benedict W. J. Irwin
Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data. 2848-2857 - Ya Chen
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
Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge. 2876-2887 - Franziska Kruger
Automated Identification of Chemical Series: Classifying like a Medicinal Chemist. 2888-2902 - Mahendra Awale
Matched Molecular Series Analysis for ADME Property Prediction. 2903-2914 - Ferruccio Palazzesi
BIreactive: A Machine-Learning Model to Estimate Covalent Warhead Reactivity. 2915-2923 - Bishnu Thapa
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
Higher Accuracy Achieved for Protein-Ligand Binding Pose Prediction by Elastic Network Model-Based Ensemble Docking. 2939-2950 - Dragos Horvath
"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
Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles. 2966-2976 - Vigneshwari Subramanian
Multisolvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors. 2977-2988 - Peter A. Hunt
Predicting pKa Using a Combination of Semi-Empirical Quantum Mechanics and Radial Basis Function Methods. 2989-2997 - Yue Zhao, Agnivo Gosai
Multiscale Modeling Reveals the Cause of Surface Stress Change on Microcantilevers Due to Alkanethiol SAM Adsorption. 2998-3008 - Irene Luque Ruiz
Prototype Selection Method Based on the Rivality and Reliability Indexes for the Improvement of the Classification Models and External Predictions. 3009-3021 - Fan Yang
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
Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. 3030-3042 - Raquel Yanes-Rodríguez
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
Fast Estimation of the Blood-Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane. 3057-3067 - Tadeo E. Saldaño
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
Accelerated Protein Folding Using Greedy-Proximal A. 3093-3104 - Santanu Santra
Insights into the Sensitivity of Arginine Concentration to Preserve the Folded Form of Insulin Monomer under Thermal Stress. 3105-3119 - Maximilian Kuhn
Assessment of Binding Affinity via Alchemical Free-Energy Calculations. 3120-3130 - Richard Bradshaw
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields? 3131-3144 - Benedetta Righino
Identification and Modeling of a GT-A Fold in the α-Dystroglycan Glycosylating Enzyme LARGE1. 3145-3156 - Massimiliano Anselmi
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase. 3157-3171 - Mohammed Benabderrahmane, Ronan Bureau
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
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
Mechanism-Based Rational Discovery and In Vitro Evaluation of Novel Microtubule Stabilizing Agents with Non-Taxol-Competitive Activity. 3204-3213 - Dan Teng
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
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
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
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
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
Structure-Based Design of Small Peptide Ligands to Inhibit Early-Stage Protein Aggregation Nucleation. 3304-3314 - Anupam Banerjee
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
Confronting Racism in Chemistry Journals. 3325-3327 - Angelica Mazzolari
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. 3328-3330 - Franziska Kruger
rdScaffoldNetwork: The Scaffold Network Implementation in RDKit. 3331-3335 - Philip N. Judson
Adapting CHMTRN (CHeMistry TRaNslator) for a New Use. 3336-3341 - Phyo Phyo Kyaw Zin
Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict? 3342-3360 - Koichiro Kato
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
Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data. 3376-3386 - Wesley K. Tatum
Generalizable Framework for Algorithmic Interpretation of Thin Film Morphologies in Scanning Probe Images. 3387-3397 - Michael E. Fortunato
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning. 3398-3407 - Xiang Gao
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
ChemStor: Using Formal Methods To Guarantee Safe Storage and Disposal of Chemicals. 3416-3422 - M. Farooq Wahab
Facile Solutions to the Problems Associated with Chemical Information and Mathematical Symbolism While Using Machine Translation Tools. 3423-3430 - Noah R. Flynn
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation. 3431-3449 - Douglas E. V. Pires
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria. 3450-3456 - Georgios A. Tritsaris
LAN: A Materials Notation for Two-Dimensional Layered Assemblies. 3457-3462 - Monica A. Silva, Alessandra S. Kiametis
Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature. 3463-3471 - Henrique M. Cezar
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method. 3472-3488 - Janet L. Paulsen
Evaluation of Free Energy Calculations for the Prioritization of Macrocycle Synthesis. 3489-3498 - Ryoma Sasaki
Acceleration of Liquid-Crystalline Phase Transition Simulations Using Selectively Scaled and Returned Molecular Dynamics. 3499-3507 - Anna S. Kamenik
Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments. 3508-3517 - Paul C. D. Hawkins
Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State. 3518-3533 - Wanlei Wei
Use of Extended-Hückel Descriptors for Rapid and Accurate Predictions of Conjugated Torsional Energy Barriers. 3534-3545 - Tom A. Young
cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest Characterization. 3546-3557 - Sohvi Luukkonen
Predicting Hydration Free Energies of the FreeSolv Database of Drug-like Molecules with Molecular Density Functional Theory. 3558-3565 - Samo Lesnik
Potential Energy Function for Fentanyl-Based Opioid Pain Killers. 3566-3576 - Genoveva Rojas, Ivana Orellana, Roberto Rosales-Rojas, Jennie García-Olivares
Structural Determinants of the Dopamine Transporter Regulation Mediated by G Proteins. 3577-3586 - Hao Li, Yeonsig Nam
Impact of A2V Mutation and Histidine Tautomerism on Aβ42 Monomer Structures from Atomistic Simulations. 3587-3592 - Ryo Hatada, Koji Okuwaki
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). 3593-3602 - Yue Zhang
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
Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding. 3632-3647 - William H. Coldren
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
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
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
vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses. 3692-3696 - Enade P. Istyastono
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
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
Learning Coarse-Grained Potentials for Binary Fluids. 3731-3745 - Peng Gao
General Protocol for the Accurate Prediction of Molecular 13C/1H NMR Chemical Shifts via Machine Learning Augmented DFT. 3746-3754 - Runyu Jing
autoBioSeqpy: A Deep Learning Tool for the Classification of Biological Sequences. 3755-3764 - Seokho Kang
Predictive Modeling of NMR Chemical Shifts without Using Atomic-Level Annotations. 3765-3769 - Lior Hirschfeld, Kyle Swanson
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. 3770-3780 - Christopher M. Baker
Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry. 3781-3791 - Natasha Kamerlin
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
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
Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory. 3843-3853 - N. Arul Murugan
Multiscale Modeling of Two-Photon Probes for Parkinson's Diagnostics Based on Monoamine Oxidase B Biomarker. 3854-3863 - Aishwary T. Shivgan, Jan K. Marzinek
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
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
Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field. 3935-3943 - Rajas Rao
Versatile Dimerisation Process of Translocator Protein (TSPO) Revealed by an Extensive Sampling Based on a Coarse-Grained Dynamics Study. 3944-3957 - Liang Xu
Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. 3958-3968 - António J. Preto
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
Conserved Luminal C-Terminal Domain Dynamically Controls Interdomain Communication in Sarcolipin. 3985-3991 - Jonathan Parkinson
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
Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics. 4021-4029 - Christopher M. Siwy
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
Integrated Binary QSAR-Driven Virtual Screening and In Vitro Studies for Finding Novel hMAO-B-Selective Inhibitors. 4047-4055 - Vinicius M. Alves
SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. 4056-4063 - Vikash Kumar
GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor. 4064-4075 - Karen R. Navarrete, Verónica A. Jiménez
Interdimeric Curvature in Tubulin-Tubulin Complexes Delineates the Microtubule-Destabilizing Properties of Plocabulin. 4076-4084 - Cong Shen
Multiview Joint Learning-Based Method for Identifying Small-Molecule-Associated MiRNAs by Integrating Pharmacological, Genomics, and Network Knowledge. 4085-4097 - Japheth E. Gado
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
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
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
DIA-DB: A Database and Web Server for the Prediction of Diabetes Drugs. 4124-4130 - William Mangione
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. 4131-4136 - Jonathan Fine, Matthew Muhoberac, Guillaume Fraux
DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening. 4137-4143 - Xin Cindy Yan
Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery. 4144-4152 - Zoe Cournia
Rigorous Free Energy Simulations in Virtual Screening. 4153-4169 - Joseph A. Morrone
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
Predicting Binding from Screening Assays with Transformer Network Embeddings. 4191-4199 - Paul G. Francoeur
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
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring. 4216-4230 - Javier Vázquez
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
Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening. 4246-4262 - Viet-Khoa Tran-Nguyen
LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening. 4263-4273 - Christoph Grebner
Virtual Screening in the Cloud: How Big Is Big Enough? 4274-4282 - Lindsey Burggraaff
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. 4283-4295 - Ann E. Cleves
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket. 4296-4310 - Phani Ghanakota
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
Fragment-Based Computational Method for Designing GPCR Ligands. 4339-4349 - Hao Liang
Discovery of Targeted Covalent Natural Products against PLK1 by Herb-Based Screening. 4350-4358 - Yan Li
Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. 4359-4375 - Francois Berenger
Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included. 4376-4387 - Lin Wei
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
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
MRP.py: A Parametrizer of Post-Translationally Modified Residues. 4424-4428 - Zhiwei Feng
Pain-CKB, A Pain-Domain-Specific Chemogenomics Knowledgebase for Target Identification and Systems Pharmacology Research. 4429-4435 - Marley L. Samways
grand: A Python Module for Grand Canonical Water Sampling in OpenMM. 4436-4441 - Pedro B. P. S. Reis, Diogo Vila-Viçosa
PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. 4442-4448 - Todd J. Wills
Impact of Chemist-In-The-Loop Molecular Representations on Machine Learning Outcomes. 4449-4456 - Alex D. Casey
Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks. 4457-4473 - Zhongliang Guo
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
Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity. 4497-4505 - Martijn Oldenhof
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning. 4506-4517 - Callum J. Court
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning. 4518-4535 - Lewis J. Martin
Comparing Fingerprints for Ligand-Based Virtual Screening: A Fast and Scalable Approach for Unbiased Evaluation. 4536-4545 - Lewis H. Mervin
Comparison of Scaling Methods to Obtain Calibrated Probabilities of Activity for Protein-Ligand Predictions. 4546-4559 - David J. Ponting
Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints. 4560-4568 - Hao Tian
ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. 4569-4581 - Domenico Alberga
De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization. 4582-4593 - Huaipan Jiang
Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. 4594-4602 - Xiting Wang
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
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
Discovery of Dual FGFR4 and EGFR Inhibitors by Machine Learning and Biological Evaluation. 4640-4652 - Anthony Difranzo
Nearest Neighbor Gaussian Process for Quantitative Structure-Activity Relationships. 4653-4663 - Lindsey Burggraaff
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. 4664-4672 - Himaghna Bhattacharjee
Thermochemical Data Fusion Using Graph Representation Learning. 4673-4683 - Ruimin Ma
PI1M: A Benchmark Database for Polymer Informatics. 4684-4690 - Kaveh Kavousi
IAMPE: NMR-Assisted Computational Prediction of Antimicrobial Peptides. 4691-4701 - Tyler B. Hughes
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. 4702-4716 - Bashir Akhlaq Akhoon, Sushil Choudhary
Discovery of a New Donepezil-like Acetylcholinesterase Inhibitor for Targeting Alzheimer's Disease: Computational Studies with Biological Validation. 4717-4729 - Carmen Esposito
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. 4730-4749 - Shao Hua Lu
Novel Approach to the Analysis of Chemical Third-Order Data. 4750-4756 - James A. Lumley
The Derivation of a Matched Molecular Pairs Based ADME/Tox Knowledge Base for Compound Optimization. 4757-4771 - Octav Caldararu, Rukmankesh Mehra
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
Findings of the Second Challenge to Predict Aqueous Solubility. 4791-4803 - Stefano Costanzi
Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis. 4804-4816 - Tárcius N. Ramos
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
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
A Genetic Algorithmic Approach to Determine the Structure of Li-Al Layered Double Hydroxides. 4845-4855 - Masoumeh Mousavi
Non-Covalent π-Stacking Interactions between Asphaltene and Porphyrin in Bitumen. 4856-4866 - Junichi Higo
Molecular Interaction Mechanism of a 14-3-3 Protein with a Phosphorylated Peptide Elucidated by Enhanced Conformational Sampling. 4867-4880 - Kenneth Goossens
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
Self-Learning Molecular Design for High Lithium-Ion Conductive Ionic Liquids using Maze Game. 4904-4911 - Mueed Ur Rahman, Ashfaq Ur Rehman
Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins. 4912-4923 - Rahul Prabhu
Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity. 4924-4957 - Ignacio Migliaro
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
Ensemble-Based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small-Molecule Ligands. 4967-4974 - Jianguo Li
Dissecting the Molecular Mechanism of Colistin Resistance in mcr-1 Bacteria. 4975-4984 - Jingyuan Zhuang, Fan Zhang, Jingwei Zhou
Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases. 4985-4994 - Nivedita Dutta
Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space. 4995-5002 - Pablo Herrera-Nieto
Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. 5003-5010 - Nabil Abid
New Insights into the Effect of Residue Mutations on the Rotavirus VP1 Function Using Molecular Dynamic Simulations. 5011-5025 - Junhao Li, Yang Zhou
Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations. 5026-5035 - Federica Cossu
Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly. 5036-5044 - Grazia Cottone
Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor. 5045-5056 - Anupam Mondal
Mechanism of Dynamic Binding of Replication Protein A to ssDNA. 5057-5069 - Daisuke Miyata
Automatic Determination of the Sequential Order of Dynamic Data and Its Application to Vibrational Spectroscopy. 5070-5079 - Olivier Sheik Amamuddy
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. 5080-5102 - Jakob Schneider
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
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
Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains. 5142-5152 - Xiaocong Wang
Insights into the Loop at the E-Selectin Binding Site: From Open to Close Conformation. 5153-5161 - Angelo Spadaro
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
In Silico Classifiers for the Assessment of Drug Proarrhythmicity. 5172-5187 - Jean-Rémy Marchand
An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. 5188-5202 - Holli-Joi Sullivan
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
Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins. 5225-5233 - Michael L. Drummond
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies. 5234-5254 - Yang Li
Protein Surface Printer for Exploring Protein Domains. 5255-5264 - Paolo Moretti
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
Correction to Prediction and Experimental Confirmation of Novel Peripheral Cannabinoid-1 Receptor Antagonists. 5282
Volume 60, Number 11, November 2020
- Kira A. Armacost
Exploring Novel Directions in Free Energy Calculations. 5283-5286 - Amy Y. Shih
Impact of Protein Preparation on Resulting Accuracy of FEP Calculations. 5287-5289 - Tharindu Senapathi
BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations. 5290-5295 - Hsu-Chun Tsai
Validation of Free Energy Methods in AMBER. 5296-5300 - Haochuan Chen
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. 5301-5307 - Lin Frank Song
Evolution of Alchemical Free Energy Methods in Drug Discovery. 5308-5318 - Julia Gebhardt, Matthias Kiesel, Sereina Riniker
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
Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies. 5331-5339 - Surl-Hee Ahn
Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. 5340-5352 - Ercheng Wang
Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities. 5353-5365 - Haohao Fu
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape. 5366-5374 - W. F. Drew Bennett
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. 5375-5381 - Hiraku Oshima
Prediction of Protein-Ligand Binding Pose and Affinity Using the gREST+FEP Method. 5382-5394 - Jan Walther Perthold
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). 5395-5406 - Gerhard König
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. 5407-5423 - Anita Plazinska
Chirality Effects in Biomolecular Systems: Calculation of the Relative Free Energies by Molecular Dynamics Simulations. 5424-5436 - Zheng Zheng
MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. 5437-5456 - Christina E. M. Schindler
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects. 5457-5474 - Samo Lesnik, Milan Hodoscek
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
Water Bridges Play a Key Role in Affinity and Selectivity for Malarial Protease Falcipain-2. 5499-5512 - Kenneth Goossens
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
Combining Monte Carlo and Molecular Dynamics Simulations for Enhanced Binding Free Energy Estimation through Markov State Models. 5529-5539 - Arghya Chakravorty
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
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. 5563-5579 - Alexander D. Wade
Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. 5580-5594 - Tai-Sung Lee
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. 5595-5623 - Saara Lautala
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.
Generative Models for Molecular Design. 5635-5636 - Maxime Langevin
Scaffold-Constrained Molecular Generation. 5637-5646 - Ke Yu
Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space. 5647-5657 - Jacques Boitreaud
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
Guidelines for Recurrent Neural Network Transfer Learning-Based Molecular Generation of Focused Libraries. 5699-5713 - Wenhao Gao
The Synthesizability of Molecules Proposed by Generative Models. 5714-5723 - Adrian J. Mulholland
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
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
Off-Patent Drug Repositioning. 5746-5753 - Sumit Kumar, Prem Prakash Sharma, Uma Shankar
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
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. 5771-5780 - Anuj Gahlawat
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease. 5781-5793 - Junjie Zou, Jian Yin
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations. 5794-5802 - Helen M. Deeks, Rebecca Walters
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
SARS-CoV-2 Main Protease: A Molecular Dynamics Study. 5815-5831 - Atanu Acharya
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. 5832-5852 - Rui Wang
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine. 5853-5865 - Ariane Nunes-Alves
What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling. 5866-5867 - Kenneth M. Merz Jr.
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. 5868-5869 - Wenxi Zhao, Dmitriy Korobskiy
Converging Interests: Chemoinformatics, History, and Bibliometrics. 5870-5872 - Gerald M. Maggiora, José L. Medina-Franco
From Qualitative to Quantitative Analysis of Activity and Property Landscapes. 5873-5880 - Felipe Rodrigues Souza
Recent Open Issues in Coarse Grained Force Fields. 5881-5884 - Igor Barden Grillo, Gabriel Aires Urquiza-Carvalho
PRIMoRDiA: A Software to Explore Reactivity and Electronic Structure in Large Biomolecules. 5885-5890 - Maho Nakata
PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties. 5891-5899 - Jinwen Shan, Xiaolin Pan
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
PySHS: Python Open Source Software for Second Harmonic Scattering. 5912-5917 - Thomas Blaschke, Josep Arús-Pous, Hongming Chen, Christian Margreitter
REINVENT 2.0: An AI Tool for De Novo Drug Design. 5918-5922 - Victor H. Rusu, Denys E. S. Santos
Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. 5923-5927 - Malte Döntgen
Atomic Partial Charges as Descriptors for Barrier Heights. 5928-5931 - Yaozong Li
Structural and Dynamic Insights into Redundant Function of YTHDF Proteins. 5932-5935 - Doyeong Hwang, Soojung Yang
Comprehensive Study on Molecular Supervised Learning with Graph Neural Networks. 5936-5945 - Nurlybek Amangeldiuly
Baseline Model for Predicting Protein-Ligand Unbinding Kinetics through Machine Learning. 5946-5956 - Elena L. Cáceres
Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction. 5957-5970 - Obaidur Rahaman
Deep Learning Total Energies and Orbital Energies of Large Organic Molecules Using Hybridization of Molecular Fingerprints. 5971-5983 - Beomchang Kang
Prediction of Molecular Electronic Transitions Using Random Forests. 5984-5994 - Pracheta Sahoo, Indranil Roy
MultiCon: A Semi-Supervised Approach for Predicting Drug Function from Chemical Structure Analysis. 5995-6006 - Vishal B. Siramshetty
Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the "Big Data" Era. 6007-6019 - Dragos Horvath
Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control. 6020-6032 - Gerardo Valadez Huerta
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
LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. 6044-6053 - Sheng Gui
Molecular Sparse Representation by a 3D Ellipsoid Radial Basis Function Neural Network via L1 Regularization. 6054-6064 - John J. Irwin
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
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
Capturing Crystal Shape Evolution from Molecular Simulations. 6109-6119 - Hans Matter
Using Graph Databases to Investigate Trends in Structure-Activity Relationship Networks. 6120-6134 - David Balcells
tmQM Dataset - Quantum Geometries and Properties of 86k Transition Metal Complexes. 6135-6146 - Donald Loveland, Bhavya Kailkhura, Piyush Karande
Automated Identification of Molecular Crystals' Packing Motifs. 6147-6154 - Sebastian Mosbach
Multiscale Cross-Domain Thermochemical Knowledge-Graph. 6155-6166 - Chun Jiang Zhu
Benchmark on Indexing Algorithms for Accelerating Molecular Similarity Search. 6167-6184 - Leila Tabrizi
Antioxidant and Anticancer Properties of Functionalized Ferrocene with Hydroxycinnamate Derivatives - An Integrated Experimental and Theoretical Study. 6185-6203 - Felipe J. Valencia
Thermal Stability of Hollow Porous Gold Nanoparticles: A Molecular Dynamics Study. 6204-6210 - Steven K. Albanese
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
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
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
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. 6269-6281 - Felipe Curtolo
Mechanisms for Flavin-Mediated Oxidation: Hydride or Hydrogen-Atom Transfer? 6282-6287 - Maria G. Khrenova
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
Benchmark of Generic Shapes for Macrocycles. 6298-6313 - Haochen Xie
Molecular Dynamics Simulations of Photo-Induced Free Radical Polymerization. 6314-6327 - Eric D. Boittier
GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans. 6328-6343 - Jordi Juárez Jiménez
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes. 6344-6354 - Jingxiao Bao, Xiao He
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
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
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
Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis. 6419-6426 - Aakash Saha
Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. 6427-6437 - Shaima Hashem
Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin. 6438-6446 - Ozge Kurkcuoglu
Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome. 6447-6461 - Suman Samantray
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. 6462-6475 - Brian D. Ratnasinghe
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.
Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. 6489-6501 - Florian Flachsenberg
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. 6502-6522 - Adolfo Bastida
On the Role of Entropy in the Stabilization of α-Helices. 6523-6531 - Riccardo Ocello, Simone Furini
Conduction and Gating Properties of the TRAAK Channel from Molecular Dynamics Simulations with Different Force Fields. 6532-6543 - Laura Chachulski
LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance. 6544-6554 - Alice Ballone, Francesca Picarazzi
Experimental and Computational Druggability Exploration of the 14-3-3ζ/SOS1pS1161 PPI Interface. 6555-6565 - Holly Freedman
Application of Molecular Dynamics Simulations to the Design of Nucleotide Inhibitors Binding to Norovirus Polymerase. 6566-6578 - Levente M. Mihalovits
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations. 6579-6594 - Andreas Tosstorff
Identification of Noncompetitive Protein-Ligand Interactions for Structural Optimization. 6595-6611 - Amanda E. Wakefield
Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. 6612-6623 - Dongxiao Hao
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
Stereospecific Inhibition of Ethanol Potentiation on Glycine Receptor by M554 Stereoisomers. 6634-6641 - Charleen G. Don
Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations. 6642-6653 - Tobias Hüfner-Wulsdorf
Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms. 6654-6665 - Phasit Charoenkwan, Janchai Yana
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
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
Identification of Small Molecule-miRNA Associations with Graph Regularization Techniques in Heterogeneous Networks. 6709-6721 - Ulf Norinder, Ola Spjuth
Correction to "Using Predicted Bioactivity Profiles to Improve Predictive Modeling". 6722
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2024-10-31 20:03 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by: