Journal of Chemical Information and Modeling

Article	Citations
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	3582
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	784
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	528
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	249
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	182
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	181
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	171
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	170
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	153
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	127
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	124
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	122
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	118
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	117
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	111
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	110
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	107
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	106
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	104
HSQC Spectra Simulation and Matching for Molecular Identification	101
Issue Publication Information	98
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19	97
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	92
Large Language Model for Automating the Analysis of Cryoprotectants	86
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	84

Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	83
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	82
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	82
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	82
Issue Publication Information	81
Issue Editorial Masthead	81
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	78
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	76
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	75
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	74
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	72
Spatially Resolved Uncertainties for Machine Learning Potentials	70
Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis	70
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	69
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	68
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	66
QM/MM Study of the Metabolic Oxidation of 6′,7′-Dihydroxybergamottin Catalyzed by Human CYP3A4: Preferential Formation of the γ-Ketoenal Product in Mechanism-Based Inactivation	66
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	66
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	64
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	64
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	64
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	64
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	63
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	63
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	62
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	61
The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-	61
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	60
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	60
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	59
Cyclosporin A: Conformational Complexity and Chameleonicity	57
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	57
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	57
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	55
Lipid Oxidation: Role of Membrane Phase-Separated Domains	53
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	52
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach	51
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	51
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	51
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	51
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	50
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	50
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	50
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	49
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	49
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	48
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	47
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	47
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	47
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	47

Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	47
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	47
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	47
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	47
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	46
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	46
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	46
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site	46
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	45
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	43
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	42
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	42
Diffusion Models in De Novo Drug Design	42
Locating Multiple Transition Pathways for Complex Biomolecules	42
Issue Editorial Masthead	42
Issue Publication Information	42
Rational Design of Nonbonded Point Charge Models for Divalent Metal Cations with Lennard-Jones 12-6 Potential	41
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations	41
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	41
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method	40
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	40
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	40
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern	40
Knowledge-Based Artificial Intelligence System for Drug Prioritization	40
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	40
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	39
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	39
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	39
Study on the Assembly Mechanisms and Transport Properties of Transmembrane End-Charged Cyclic Peptide Nanotubes	39
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	39
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	39
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	39
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	38
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	38
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	38
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	37
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	37
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	37
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	37
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	37
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	37
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach	37
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	37
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	37
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	37
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	37
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	36
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	36
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	36
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	36
af3cli: Streamlining AlphaFold3 Input Preparation	36
Correction to “XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties”	35
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	35
QM/MM Study of Human Transketolase: Thiamine Diphosphate Activation Mechanism and Complete Catalytic Cycle	35
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	35
Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set	35
Special Issue on Reaction Informatics and Chemical Space	34
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	34
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	34
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	33
Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder	33
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	33
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	33
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	33
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	33
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	33
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	33
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	33
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	32
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	32
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	32
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	32
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	32
Multiple Interactions of Glucose with the Extra-Membranous Loops of GLUT1 Aid Transport	32
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	32
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	32
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	32
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning	32
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	32
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	32

Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	31
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	31
Atomic Polarizabilities for Interactive Dipole Induction Models	31
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	31
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	31
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	31
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	31
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	31
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	31
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	31
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	31
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	30
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	30
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	30
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	30
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	30
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	30
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	30
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	30
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	29
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	29
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking	29
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	29
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	29
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	29
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	29
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	29
Large-Scale Modeling of Sparse Protein Kinase Activity Data	29
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	28
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	28
Activity Regulation and Conformation Response of Janus Kinase 3 Mediated by Phosphorylation: Exploration from Correlation Network Analysis and Markov Model	28
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease	28
All-Atom Membrane Builder via Multiscale Simulation	28
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets	28
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	28
Clustering of Synthetic Routes Using Tree Edit Distance	28
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	28
Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor	27
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	27
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	27
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	27
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	27
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	27
Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study	27
Exploring the Potential of Adaptive, Local Machine Learning in Comparison to the Prediction Performance of Global Models: A Case Study from Bayer’s Caco-2 Permeability Database	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	27
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	26
Issue Publication Information	26
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	26
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	26
Issue Publication Information	26
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	26
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	26
Issue Editorial Masthead	26
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	26
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	25
Issue Editorial Masthead	25
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction	25
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations	25
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	25
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	25
Issue Editorial Masthead	25
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	25
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	25
Exploring the Substrate-Assisted Dehydration of Chorismate Catalyzed by Dehydratase MqnA from QM/MM Calculations: The Role of Pocket Residues and the Hydrolysis Mechanism of N17D Mutant	25
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	25
Issue Publication Information	25
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	25
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	25
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	24
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	24
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	24
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting	24
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	24
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors	24
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein	24
Preventing AI From Creating Biochemical Threats	24
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes	24
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease Mpro and Papain-like Protease PLpro of SARS-CoV-2	24
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro	24
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests	24
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations	24
Kick–Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction	24
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study	24
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity	24
Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations	23
Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants	23
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	23
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions	23
Issue Editorial Masthead	23
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	23
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	23
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	23
Issue Editorial Masthead	23
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity	23