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	1028
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	540
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	294
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	250
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	200
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	150
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	146
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	144
HSQC Spectra Simulation and Matching for Molecular Identification	135
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	131
Large Language Model for Automating the Analysis of Cryoprotectants	127
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	126
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	120
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	114
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	107
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	98
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	97
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	94
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	94
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	91
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	89
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	89
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	84
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	82
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	81

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	81
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	79
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	78
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	77
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	77
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site	76
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	76
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	74
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	73
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-	73
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	73
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	73
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	72
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	72
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	72
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	71
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	71
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	63
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	59
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	59
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	57
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	57
Issue Publication Information	56
Issue Publication Information	56
Issue Editorial Masthead	56
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	55
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	55
Cyclosporin A: Conformational Complexity and Chameleonicity	54
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	54
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	53
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	53
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	52
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	52
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	51
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	51
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	51
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	50
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	48
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	48
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	48
Recommendations to Improve Text-Based Representation Systems for Polyolefins	48
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	47
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	47
Issue Publication Information	46
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	46
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	45
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	45
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	45
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	45
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	45

Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	45
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	45
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	45
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	44
Diffusion Models in De Novo Drug Design	44
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach	43
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	43
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	43
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	43
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	42
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	42
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	42
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	42
Spatially Resolved Uncertainties for Machine Learning Potentials	42
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	42
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	42
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	42
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	42
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	41
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	41
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	41
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	40
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	40
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	40
Locating Multiple Transition Pathways for Complex Biomolecules	39
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	39
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	39
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	38
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	38
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	38
Knowledge-Based Artificial Intelligence System for Drug Prioritization	38
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	38
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	38
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	37
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	37
Correction to “XGraphBoost: Extracting Graph Neural Network-Based Features for a Better Prediction of Molecular Properties”	37
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	36
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	36
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	36
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	36
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	36
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	36
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	36
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	36
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	36
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	36
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	35
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	35
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	35
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	35
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	35
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	35
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	35
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	35
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	35
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern	35
Solvation Energetic Costs of Cognate Binding Site Formation	35
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	34
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	34
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	34
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	34
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	34
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	33
af3cli: Streamlining AlphaFold3 Input Preparation	33
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method	33
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	33
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	33
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	33
Atomic Polarizabilities for Interactive Dipole Induction Models	33
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	32
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	32
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	32
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	32
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	32
Special Issue on Reaction Informatics and Chemical Space	32
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	32
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	32
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations	31
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	31
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	31

Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	31
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	31
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	31
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	30
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	30
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	30
Issue Publication Information	30
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	30
Issue Editorial Masthead	30
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach	30
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	30
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	29
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	29
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	29
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	29
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	29
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	29
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	29
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	29
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	29
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	28
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	28
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	28
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	28
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	28
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	28
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	28
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	28
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	28
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	27
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	27
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	27
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	27
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	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
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	27
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	27
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	27
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	27
All-Atom Membrane Builder via Multiscale Simulation	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	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	26
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	26
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	26
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	26
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting	26
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	26
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	26
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations	26
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein	26
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	26
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	26
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	26
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	26
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	25
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking	25
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	25
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus	25
Issue Editorial Masthead	25
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	25
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	25
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	25
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	25
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	25
Issue Editorial Masthead	25
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	25
Large-Scale Modeling of Sparse Protein Kinase Activity Data	25
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	25
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors	25
Issue Publication Information	25
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	25
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	24
Ensemble Docking for Intrinsically Disordered Proteins	24
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	24
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	24
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity	24
Issue Publication Information	24
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	24
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	24
Preventing AI From Creating Biochemical Threats	24
Issue Publication Information	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
TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms	24
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	24
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	23
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro	23
Computer-Aided Design and Synthesis of a New Class of PEX14 Inhibitors: Substituted 2,3,4,5-Tetrahydrobenzo[F][1,4]oxazepines as Potential New Trypanocidal Agents	23
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	23
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	23
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	23
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets	23
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	23
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	23
Synergistic Effects of Natural Compounds Toward Inhibition of SARS-CoV-2 3CL Protease	23
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	23