Journal of Chemical Information and Modeling

Article	Citations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings	2270
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance	491
AmberTools	270
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	161
MolGPT: Molecular Generation Using a Transformer-Decoder Model	160
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation	155
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function	139
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19	135
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation	128
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	120
Artificial Intelligence in Chemistry: Current Trends and Future Directions	119
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models	109
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation	105
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network	102
Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis	101
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations	88
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta	85
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature	84
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning	83
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	81
Chemprop: A Machine Learning Package for Chemical Property Prediction	80
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides	77
Recent Force Field Strategies for Intrinsically Disordered Proteins	76
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations	76
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling	75

Generative Deep Learning for Targeted Compound Design	71
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro	71
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields	71
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning	69
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate	68
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs	68
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations	67
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits	66
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression	65
Exploration of Ultralarge Compound Collections for Drug Discovery	63
Quantum Machine Learning Algorithms for Drug Discovery Applications	63
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor	63
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles	62
Computational Methods and Tools in Antimicrobial Peptide Research	61
SMILES to Smell: Decoding the Structure–Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach	60
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction	59
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning	59
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science	59
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro	58
tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal Complexes	58
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems	58
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery	58
Property-Unmatched Decoys in Docking Benchmarks	57
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro	56
N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study	56
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations	55
RMG Database for Chemical Property Prediction	54
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design	54
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning	53
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges	52
Artificial Intelligence in Drug Toxicity Prediction: Recent Advances, Challenges, and Future Perspectives	52
Making it Rain: Cloud-Based Molecular Simulations for Everyone	52
Informatics for Chemistry, Biology, and Biomedical Sciences	51
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment	51
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters	50
SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning	50
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization	50
XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties	49
GGL-Tox: Geometric Graph Learning for Toxicity Prediction	49
SolTranNet–A Machine Learning Tool for Fast Aqueous Solubility Prediction	49
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks	49
Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity	49
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design	48
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes	48
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease	48
Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy	46
AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides	46
DeepBSP—a Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures	46
Do Large Language Models Understand Chemistry? A Conversation with ChatGPT	46
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods	45

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery	45
A General Picture of Cucurbit[8]uril Host–Guest Binding	45
Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study	44
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions	43
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites	43
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations	43
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry	43
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering	43
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics	42
Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking	42
Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein–Protein Docking, Molecular Dynamics, and MM-GBSA Calculations	42
Automated Chemical Reaction Extraction from Scientific Literature	41
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	41
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard	40
Permutation Invariant Graph-to-Sequence Model for Template-Free Retrosynthesis and Reaction Prediction	40
Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks	40
Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields	40
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites	40
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1	40
Predicting Infrared Spectra with Message Passing Neural Networks	40
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design	40
Predicting Protein–Ligand Docking Structure with Graph Neural Network	39
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening	39
Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures	38
Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning	38
AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional Networks	38
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease	38
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions	37
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations	37
Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations	37
Deep Learning-Based Conformal Prediction of Toxicity	37
Search for ABO3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies	37
Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns	37
A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses	37
Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction	37
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids	36
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	36
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement	36
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design	36
Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the “Big Data” Era	36
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method	36
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables	35
True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better	35
Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set	35
The (Re)-Evolution of Quantitative Structure–Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods	35
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast	35
De Novo Structure-Based Drug Design Using Deep Learning	35
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex	34
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations	34
Scaffold-Constrained Molecular Generation	34
Dielectric Polymer Property Prediction Using Recurrent Neural Networks with Optimizations	34
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study	34
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease	34
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction	33
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis	33
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures	33
Machine Learning Models Identify Inhibitors of SARS-CoV-2	33
Cyclosporin A: Conformational Complexity and Chameleonicity	33
Vina-GPU 2.0: Further Accelerating AutoDock Vina and Its Derivatives with Graphics Processing Units	33
Mining Insights on Metal–Organic Framework Synthesis from Scientific Literature Texts	32
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning	32
Pairwise Difference Regression: A Machine Learning Meta-algorithm for Improved Prediction and Uncertainty Quantification in Chemical Search	32
Explainable Deep Relational Networks for Predicting Compound–Protein Affinities and Contacts	32
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions	32
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization	32
Comparative Study of Deep Generative Models on Chemical Space Coverage	32
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design	32
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations	32
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER	32
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations	31
Ligand Strain Energy in Large Library Docking	31
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces	31
Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation	31
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	31
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms	31
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps	31
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3	30
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening	30
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes	30
Density Prediction Models for Energetic Compounds Merely Using Molecular Topology	30

Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins bycorrelationplus	30
Generative Chemical Transformer: Neural Machine Learning of Molecular Geometric Structures from Chemical Language via Attention	30
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics	30
Selecting Collective Variables and Free-Energy Methods for Peptide Translocation across Membranes	30
MoleGuLAR: Molecule Generation Using Reinforcement Learning with Alternating Rewards	30
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	30
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	30
Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence	29
Classification Model for the Second Extracellular Loop of Class A GPCRs	29
Diversity and Chemical Library Networks of Large Data Sets	29
SGTPy: A Python Code for Calculating the Interfacial Properties of Fluids Based on the Square Gradient Theory Using the SAFT-VR Mie Equation of State	29
Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau	28
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profil	28
Kernel Methods for Predicting Yields of Chemical Reactions	28
MGCVAE: Multi-Objective Inverse Design via Molecular Graph Conditional Variational Autoencoder	28
Deep Learning Model for Efficient Protein–Ligand Docking with Implicit Side-Chain Flexibility	28
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	28
BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization	28
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning	28
Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and In Vitro Study	28
A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Predictions: New Opportunities and Challenges for Drug Discovery	28
Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method	27
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity	27
pdCSM-cancer: Using Graph-Based Signatures to Identify Small Molecules with Anticancer Properties	27
Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes	27
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern	27
Qualitative Estimation of Protein–Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations	27
Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK	27
PyRMD: A New Fully Automated AI-Powered Ligand-Based Virtual Screening Tool	27
GlycoTorch Vina: Docking Designed and Tested for Glycosaminoglycans	26
Editorial: Method and Data Sharing and Reproducibility of Scientific Results	26
Protein–Peptide Binding Site Detection Using 3D Convolutional Neural Networks	26
Importance of Three-Body Problems and Protein–Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations	26
Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus	26
Understanding Ring Puckering in Small Molecules and Cyclic Peptides	26
A Differentiable Neural-Network Force Field for Ionic Liquids	25
Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides	25
DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization	25
Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API	25
Substituent Effect on the Photophysics and ESIPT Mechanism ofN,N′-Bis(salicylidene)-p-phenylenediamine: A DFT/TD-DFT Analysis	25
De Novo Molecule Design Using Molecular Generative Models Constrained by Ligand–Protein Interactions	25
GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network	25
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures	25
DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design	25
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study	25
Machine Learning on DNA-Encoded Library Count Data Using an Uncertainty-Aware Probabilistic Loss Function	25
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening	25
Molecular Dynamics Simulations and Diversity Selection by Extended Continuous Similarity Indices	25
NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes	25
AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge	24
Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials	24
Transfer Learned Designer Polymers For Organic Solar Cells	24
Bringing Structural Implications and Deep Learning-Based Drug Identification for KRAS Mutants	24
Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S	24
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields	24
Electron-Passing Neural Networks for Atomic Charge Prediction in Systems with Arbitrary Molecular Charge	24
iCYP-MFE: Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding	24
Machine Learning-Assisted Carbon Dot Synthesis: Prediction of Emission Color and Wavelength	24
Three Simple Properties Explain Protein Stability Change upon Mutation	24
ITScore-NL: An Iterative Knowledge-Based Scoring Function for Nucleic Acid–Ligand Interactions	24
Quantitative Kinetic Model of CO2 Absorption in Aqueous Tertiary Amine Solvents	23
Representing Polymers as Periodic Graphs with Learned Descriptors for Accurate Polymer Property Predictions	23
MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation	23
Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function	23
Emerging Landscape of Computational Modeling in Pharmaceutical Development	23
Application of Machine Learning in Spatial Proteomics	23
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein–Ligand Binding Affinity Prediction	23
NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics	23
Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors	23
Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes	23
Elucidation of Structural Determinants Delineates the Residues Playing Key Roles in Differential Dynamics and Selective Inhibition of Sirt1–3	23
HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention	23
Few-Shot Learning for Low-Data Drug Discovery	23
DeLA-Drug: A Deep Learning Algorithm for Automated Design of Druglike Analogues	23
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs	23
Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation	23
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures	22
FragRep: A Web Server for Structure-Based Drug Design by Fragment Replacement	22
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units	22
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network	22
Learning Atomic Interactions through Solvation Free Energy Prediction Using Graph Neural Networks	22
Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid–Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain	22
New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves	22
Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions	22
TorsionNet: A Deep Neural Network to Rapidly Predict Small-Molecule Torsional Energy Profiles with the Accuracy of Quantum Mechanics	22
Yuel: Improving the Generalizability of Structure-Free Compound–Protein Interaction Prediction	22
PyPEF—An Integrated Framework for Data-Driven Protein Engineering	22
Machine Learning-Enabled Pipeline for Large-Scale Virtual Drug Screening	22
Multiscale Cross-Domain Thermochemical Knowledge-Graph	21
Magic Rings: Navigation in the Ring Chemical Space Guided by the Bioactive Rings	21
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2	21
Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields	21
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	21
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	21
Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling	21