Journal of Chemical Information and Modeling

Article	Citations
Issue Publication Information	1820
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	490
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	255
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	243
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	216
Issue Publication Information	205
Issue Editorial Masthead	183
Issue Publication Information	170
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	135
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	133
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	131
Adsorption Energy Prediction Model for CO 2 Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements	123
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	120
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	112
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	109
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	108
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	107
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	106
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	106
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	105
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	104
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	102
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	99
EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation	98
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	93

Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	92
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	91
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	88
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	82
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	79
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	78
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	78
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	75
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	75
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	75
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	75
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	74
Generative AI Uncovers Novel Chrebp/Txnip Axis Inhibitors with Potential Anti-inflammatory Activity	74
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	73
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	69
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	68
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	68
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	67
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	66
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	66
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	65
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	63
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	63
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	63
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	63
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	63
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	63
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	62
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	62
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	60
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	60
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	59
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	58
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	58
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	58
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	57
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	57
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	55
MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation	55
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	55
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	54
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	54
Diffusion Models in De Novo Drug Design	54
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	53
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	53
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	52
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	51
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	50
Spatially Resolved Uncertainties for Machine Learning Potentials	50
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	50

Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	49
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	49
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	49
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	48
Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding	48
Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants	48
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	48
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	48
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	48
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	48
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	47
Large Language Model for Automating the Analysis of Cryoprotectants	46
KGG : Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	46
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	46
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	45
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	45
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	45
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	45
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	44
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	44
HSQC Spectra Simulation and Matching for Molecular Identification	44
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	44
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	44
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids	44
Generative Artificial Intelligence Optimization of Albumin Binders: Coumarin and Fatty Acid Derivatives	43
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	43
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	43
Locating Multiple Transition Pathways for Complex Biomolecules	43
Recommendations to Improve Text-Based Representation Systems for Polyolefins	43
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	43
af3cli: Streamlining AlphaFold3 Input Preparation	42
Issue Publication Information	42
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein	42
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	41
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	41
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	41
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	41
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	40
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	40
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	40
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	40
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	40
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	39
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	39
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C–H Bonds Catalyzed by the Heterobimetallic Manganese–Iron Hydroxylase AibH1H2 from Rhodococcus	39
ncProFormer: A CNN-enhanced Transformer for ncRNA Coding-Potential Prediction	39
Knowledge-Based Artificial Intelligence System for Drug Prioritization	39
Energy-Guided Denoising Contrastive Learning for Molecular Property Prediction	39
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	39
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	38
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	38
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	38
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	37
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry	37
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	37
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	37
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	37
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	37
PymolFold: A PyMOL Plugin for API-Driven Structure Prediction and Quality Assessment	37
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	37
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	36
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	36
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	36
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	36
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	36
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	36
Modeling Enzyme Temperature Stability from Sequence Segment Perspective	36
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	36
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	36
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	35
F-Site: Recognizing Fluorination Patterns in Small-Molecule Drugs via a Two-Stage Transformer-Based Model	35
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	35
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	35
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	35
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	35
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery	35
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	35
Machine Learning-Based Soft Voting Ensemble Model for the Prediction of Oral Drug-Likeness of Chemical Structures	35
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	34
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	34

Comparative Binding Analysis by Computational Methods and Quartz Crystal Microbalance: Case of hnRNPA2B1 Protein and Irinotecan Drug	34
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	34
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	34
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	34
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	34
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	34
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	34
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	33
ThermoPred: AI-Enhanced Quantum Chemistry Data Set and ML Toolkit for Thermochemical Properties of API-Like Compounds and Their Degradants	33
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	33
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	33
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	33
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	33
EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design	33
ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability Prediction	33
AI-Guided Conformational Dynamics of p53 L1 Loop Reveal an Allosteric Switch Regulating DNA Binding and Cancer Hotspots	32
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	32
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	32
Computational Study of Heme b 595 to Heme d Electron Transfer in	32
CompBind: Complex Guided Pretraining-Based Structure-Free Protein–Ligand Affinity Prediction	32
Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design	32
Solvation Energetic Costs of Cognate Binding Site Formation	31
Mathematical State Function Structure Matters in Metal Oxide Reduction Thermodynamic Modeling	31
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	31
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	31
Rational Design of Single-Phase High-Entropy Oxides via Large Language Model Data Mining and Explainable Machine Learning	31
Precision-Guarded Graph–Text Alignment for Universal Chemical Understanding	31
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	31
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	31
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	31
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	30
pepADMET: A Novel Computational Platform For Systematic ADMET Evaluation of Peptides	30
Issue Publication Information	30
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	30
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	30
Integrative Computational Prediction Strategy for Antibody–Antigen Binding: A Case Study on Interleukin-1 Beta	30
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	30
Issue Publication Information	30
Issue Editorial Masthead	30
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	30
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	30
Classifying Multistate DNA Origami: An Automated Approach with Minimal Labeling and Confidence-Based Filtering	30
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	30
Issue Editorial Masthead	30
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	30
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	30
SSIF-Affinity: Multimodal Deep Learning of Sequence-Structure Features for Precise Protein–Protein Binding Affinity Prediction	30
Enhanced and Classical MD Simulations Map Aggregation-Prone Regions in the Olfactomedin Domain of Myocilin	29
Correction to “Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond”	29
Issue Editorial Masthead	29
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	29
All-Atom Membrane Builder via Multiscale Simulation	29
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	29
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	29
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting	29
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	29
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	29
Computational Insights into the Regioselective Hydroxylation of Nirmatrelvir Metabolized by Cytochrome P450 3A4	29
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL	29
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	28
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	28
Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors	28
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations	28
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification	28
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	28
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	28
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	28
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	28
Cyclin-E/A/CDK1/2 Kinetic Landscapes Drive Cell Cycle Phase-Specific Progression and Guide Cyclin-E Degradation Strategy	28
Issue Publication Information	28
HlightReaxMD: A Machine Learning-Augmented Multiscale Analysis Framework for Radiation Chemistry Dynamics and Damage Prediction	27
Polarizable AMOEBA Model for Simulating Mg 2+ ·Protein·Nucleotide Complexes	27
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	27
MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations	27
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study	27
Mapping Still Matters: Coarse-Graining with Machine Learning Potentials	27
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	27
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	27
Traj2Relax: A Trajectory-Supervised Method for Robust Structure Relaxation	27
Ensemble Docking for Intrinsically Disordered Proteins	27
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	27
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	27
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	27
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	27
CAHNetF-DTP: A Community-Aware Heterogeneous Network-Based Embedding Framework for Drug-Target Interaction Prediction	26
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design	26
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	26
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	26
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	26
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	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 Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	26
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	26
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	26