Journal of Chemical Information and Modeling

Article	Citations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings	1511
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance	455
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study	328
ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery	321
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery	180
REINVENT 2.0: An AI Tool for De Novo Drug Design	167
The Synthesizability of Molecules Proposed by Generative Models	148
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials	145
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects	140
Deep Dive into Machine Learning Models for Protein Engineering	133
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	133
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction	127
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19	125
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation	119
Rigorous Free Energy Simulations in Virtual Screening	115
Evaluating Scalable Uncertainty Estimation Methods for Deep Learning-Based Molecular Property Prediction	113
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease	112
Assessment of Binding Affinity via Alchemical Free-Energy Calculations	111
SARS-CoV-2 Main Protease: A Molecular Dynamics Study	108
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function	108
MolGPT: Molecular Generation Using a Transformer-Decoder Model	107
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes	105
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation	98
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design	98
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation	98

Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	94
LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening	89
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	85
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies	85
Artificial Intelligence in Chemistry: Current Trends and Future Directions	83
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations	83
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine	82
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models	81
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)	80
Generative Network Complex for the Automated Generation of Drug-like Molecules	79
MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network	79
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies	78
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides	76
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease	75
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta	71
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling	70
PI1M: A Benchmark Database for Polymer Informatics	70
Evolution of Alchemical Free Energy Methods in Drug Discovery	67
Deep Learning-Based Imbalanced Data Classification for Drug Discovery	65
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro	65
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning	63
Recent Force Field Strategies for Intrinsically Disordered Proteins	63
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning	62
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro	62
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields	61
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	61
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature	60
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations	59
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides	59
Generative Deep Learning for Targeted Compound Design	57
AmberTools	56
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning	55
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks	55
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19	55
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	55
De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization	54
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations	54
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate	53
General Protocol for the Accurate Prediction of Molecular 13C/1H NMR Chemical Shifts via Machine Learning Augmented DFT	53
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations	53
Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape	53
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro	52
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery	52
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro	50
Computational Methods and Tools in Antimicrobial Peptide Research	50
Comparison and Evaluation of Force Fields for Intrinsically Disordered Proteins	50
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits	50
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction	50
SMILES to Smell: Decoding the Structure–Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach	50
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning	50

BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression	49
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor	49
Exploration of Ultralarge Compound Collections for Drug Discovery	49
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems	48
Property-Unmatched Decoys in Docking Benchmarks	48
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles	47
Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations	47
IAMPE: NMR-Assisted Computational Prediction of Antimicrobial Peptides	47
tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal Complexes	46
Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment	45
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease	45
What Are the Odds of Finding a COVID-19 Drug from a Lab Repurposing Screen?	45
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations	45
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science	44
Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation	43
Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning	43
Informatics for Chemistry, Biology, and Biomedical Sciences	42
OptiMol: Optimization of Binding Affinities in Chemical Space for Drug Discovery	42
GGL-Tox: Geometric Graph Learning for Toxicity Prediction	42
Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a	42
Quantum Machine Learning Algorithms for Drug Discovery Applications	42
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method	42
XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties	41
Improving the Performance of MM/PBSA in Protein–Protein Interactions via the Screening Electrostatic Energy	41
Prediction of Energetic Material Properties from Electronic Structure Using 3D Convolutional Neural Networks	41
OpenChem: A Deep Learning Toolkit for Computational Chemistry and Drug Design	41
Making it Rain: Cloud-Based Molecular Simulations for Everyone	41
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs	40
Binding Affinity Prediction by Pairwise Function Based on Neural Network	40
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning	40
Improving Docking-Based Virtual Screening Ability by Integrating Multiple Energy Auxiliary Terms from Molecular Docking Scoring	40
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks	40
Interaction Nature and Computational Methods for Halogen Bonding: A Perspective	39
De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites	39
Insight into the LFA-1/SARS-CoV-2 Orf7a Complex by Protein–Protein Docking, Molecular Dynamics, and MM-GBSA Calculations	39
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design	39
A Machine Learning Bioinformatics Method to Predict Biological Activity from Biosynthetic Gene Clusters	39
SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning	38
Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening	38
Lean-Docking: Exploiting Ligands’ Predicted Docking Scores to Accelerate Molecular Docking	38
DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks	38
Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD	37
Structural and Dynamic Insights into Redundant Function of YTHDF Proteins	37
DeepBSP—a Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures	37
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning	37
Molassembler: Molecular Graph Construction, Modification, and Conformer Generation for Inorganic and Organic Molecules	37
Systematic Investigation of the Data Set Dependency of Protein Stability Predictors	37
Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data	36
AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides	36
SolTranNet–A Machine Learning Tool for Fast Aqueous Solubility Prediction	36
Guidelines for Recurrent Neural Network Transfer Learning-Based Molecular Generation of Focused Libraries	36
A General Picture of Cucurbit[8]uril Host–Guest Binding	36
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard	35
BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations	35
Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study	35
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods	35
PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties	35
Neural Message Passing for NMR Chemical Shift Prediction	35
AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges	35
Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data	35
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry	34
Predicting Infrared Spectra with Message Passing Neural Networks	34
PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations	34
In Silico Screening-Based Discovery of Novel Inhibitors of Human Cyclic GMP–AMP Synthase: A Cross-Validation Study of Molecular Docking and Experimental Testing	34
Nanomaterial Synthesis Insights from Machine Learning of Scientific Articles by Extracting, Structuring, and Visualizing Knowledge	34
Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity	34
Chemistry42: An AI-Driven Platform for Molecular Design and Optimization	34
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions	34
Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1	34
Multilabel Classification Models for the Prediction of Cross-Coupling Reaction Conditions	34
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning	34
Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation	33
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket	33
Structural Assessment of Agonist Efficacy in the μ-Opioid Receptor: Morphine and Fentanyl Elicit Different Activation Patterns	33
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes	33
Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method	33
Structure-Based de Novo Molecular Generator Combined with Artificial Intelligence and Docking Simulations	33
Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites	32
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria	32
NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering	32

ADME Prediction with KNIME: Development and Validation of a Publicly Available Workflow for the Prediction of Human Oral Bioavailability	32
Strengths and Weaknesses of Docking Simulations in the SARS-CoV-2 Era: the Main Protease (Mpro) Case Study	32
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics	32
Scaffold-Constrained Molecular Generation	32
A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses	31
New Trends in Virtual Screening	31
Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization	31
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery	31
Halogenated Baicalein as a Promising Antiviral Agent toward SARS-CoV-2 Main Protease	31
Findings of the Second Challenge to Predict Aqueous Solubility	31
Machine Learning Models Identify Inhibitors of SARS-CoV-2	30
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	30
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates	30
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients	30
Do Large Language Models Understand Chemistry? A Conversation with ChatGPT	30
Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields	30
Prediction of Molecular Electronic Transitions Using Random Forests	30
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease	30
Extending the Martini Coarse-Grained Force Field to N-Glycans	29
Explainable Deep Relational Networks for Predicting Compound–Protein Affinities and Contacts	29
The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?	29
Improving Enzyme Optimum Temperature Prediction with Resampling Strategies and Ensemble Learning	29
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction	29
Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity	29
Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies	29
Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the “Big Data” Era	29
Structure-Aware Multimodal Deep Learning for Drug–Protein Interaction Prediction	29
Search for ABO3 Type Ferroelectric Perovskites with Targeted Multi-Properties by Machine Learning Strategies	29
True Accuracy of Fast Scoring Functions to Predict High-Throughput Screening Data from Docking Poses: The Simpler the Better	29
Improving Few- and Zero-Shot Reaction Template Prediction Using Modern Hopfield Networks	29
Valid, Plausible, and Diverse Retrosynthesis Using Tied Two-Way Transformers with Latent Variables	29
Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning	29
RMG Database for Chemical Property Prediction	28
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein–Ligand Scoring Functions	28
Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server	28
Dielectric Polymer Property Prediction Using Recurrent Neural Networks with Optimizations	28
Comparative Study of Deep Generative Models on Chemical Space Coverage	28
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning	28
Ligand Strain Energy in Large Library Docking	28
Fast Estimation of the Blood–Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane	28
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast	28
Deep Learning-Based Conformal Prediction of Toxicity	28
VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein–Ligand Binding Free Energy Calculations	28
GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds	28
LibINVENT: Reaction-based Generative Scaffold Decoration for in Silico Library Design	28
Automated Chemical Reaction Extraction from Scientific Literature	27
General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps	27
Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set	27
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	27
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	27
Mining Insights on Metal–Organic Framework Synthesis from Scientific Literature Texts	27
BIreactive: A Machine-Learning Model to Estimate Covalent Warhead Reactivity	27
Comparison of Chemical Structure and Cell Morphology Information for Multitask Bioactivity Predictions	27
Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function	27
Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations	26
Kernel Methods for Predicting Yields of Chemical Reactions	26
Cyclosporin A: Conformational Complexity and Chameleonicity	26
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	26
Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis	26
Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and In Vitro Study	26
Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method	26
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations	26
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	26
Applications of Machine Learning to In Silico Quantification of Chemicals without Analytical Standards	26
cgbind: A Python Module and Web App for Automated Metallocage Construction and Host–Guest Characterization	26
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	26
BatteryBERT: A Pretrained Language Model for Battery Database Enhancement	25
DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design	25
De Novo Structure-Based Drug Design Using Deep Learning	25
Density Prediction Models for Energetic Compounds Merely Using Molecular Topology	25
MoleGuLAR: Molecule Generation Using Reinforcement Learning with Alternating Rewards	25
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening	25
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern	25
Misfolding and Self-Assembly Dynamics of Microtubule-Binding Repeats of the Alzheimer-Related Protein Tau	25
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids	25
Supramolecular Organization of SARS-CoV and SARS-CoV-2 Virions Revealed by Coarse-Grained Models of Intact Virus Envelopes	25
Classification Model for the Second Extracellular Loop of Class A GPCRs	25
Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex	24
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER	24
Accurate Prediction of Aqueous Free Solvation Energies Using 3D Atomic Feature-Based Graph Neural Network with Transfer Learning	24
R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study	24
Shedding Light on the Inhibitory Mechanisms of SARS-CoV-1/CoV-2 Spike Proteins by ACE2-Designed Peptides	24
FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method	24
Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles	24
TeroKit: A Database-Driven Web Server for Terpenome Research	24
Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures	24
Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery	24
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity	24
grand: A Python Module for Grand Canonical Water Sampling in OpenMM	24
Diversity and Chemical Library Networks of Large Data Sets	24
Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics	23
Molecular Perception for Visualization and Computation: The Proxima Library	23
Deep Learning Total Energies and Orbital Energies of Large Organic Molecules Using Hybridization of Molecular Fingerprints	23
Topological Similarity Search in Large Combinatorial Fragment Spaces	23
Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening	23