Journal of Chemical Information and Modeling

Article	Citations
Issue Publication Information	1742
Recommendations to Improve Text-Based Representation Systems for Polyolefins	466
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	242
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	231
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	212
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	196
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	179
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	166
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	131
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	130
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	130
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	118
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids	117
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	109
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	109
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	108
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	107
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	106
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	103
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	103
Issue Publication Information	99
Issue Editorial Masthead	98
Issue Publication Information	98
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	96
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	95

Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	90
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	89
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	86
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	78
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	76
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	76
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	74
KGG : Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	73
Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants	73
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	72
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	72
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	71
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	71
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	70
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	70
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	67
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	67
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	66
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	66
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	65
Generative AI Uncovers Novel Chrebp/Txnip Axis Inhibitors with Potential Anti-inflammatory Activity	64
Spatially Resolved Uncertainties for Machine Learning Potentials	63
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	62
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	62
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	62
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	62
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	61
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	60
Diffusion Models in De Novo Drug Design	60
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	60
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	60
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	59
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	59
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	59
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	59
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	58
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	57
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	56
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	55
Large Language Model for Automating the Analysis of Cryoprotectants	55
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	54
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	53
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	53
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	53
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	52
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	52
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	52
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	52
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	51
Adsorption Energy Prediction Model for CO 2 Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements	51

ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	49
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	49
EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation	49
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	49
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	49
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	49
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	48
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	48
HSQC Spectra Simulation and Matching for Molecular Identification	48
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	47
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	46
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	46
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	46
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	46
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	46
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	45
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	45
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
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	45
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	44
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	44
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	44
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	43
Locating Multiple Transition Pathways for Complex Biomolecules	43
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	43
MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation	43
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	43
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	43
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	43
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	43
Special Issue on Reaction Informatics and Chemical Space	42
af3cli: Streamlining AlphaFold3 Input Preparation	42
Issue Publication Information	42
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	42
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	41
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	41
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein	41
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	40
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	40
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	40
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	40
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	40
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	39
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	39
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	39
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	39
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	38
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C–H Bonds Catalyzed by the Heterobimetallic Manganese–Iron Hydroxylase AibH1H2 from Rhodococcus	38
ncProFormer: A CNN-enhanced Transformer for ncRNA Coding-Potential Prediction	38
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	38
Knowledge-Based Artificial Intelligence System for Drug Prioritization	38
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	38
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	38
Energy-Guided Denoising Contrastive Learning for Molecular Property Prediction	38
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	37
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	37
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	37
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	37
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	37
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	36
PymolFold: A PyMOL Plugin for API-Driven Structure Prediction and Quality Assessment	36
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	36
Modeling Enzyme Temperature Stability from Sequence Segment Perspective	36
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	36
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	36
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	36
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	36
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	36
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
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	35
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery	35
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	35
F-Site: Recognizing Fluorination Patterns in Small-Molecule Drugs via a Two-Stage Transformer-Based Model	35
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	34
ThermoPred: AI-Enhanced Quantum Chemistry Data Set and ML Toolkit for Thermochemical Properties of API-Like Compounds and Their Degradants	34
ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability Prediction	34
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	34
EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design	34
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	33

AI-Guided Conformational Dynamics of p53 L1 Loop Reveal an Allosteric Switch Regulating DNA Binding and Cancer Hotspots	33
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	33
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	33
Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design	33
CompBind: Complex Guided Pretraining-Based Structure-Free Protein–Ligand Affinity Prediction	33
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	33
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	33
Computational Study of Heme b 595 to Heme d Electron Transfer in	33
Solvation Energetic Costs of Cognate Binding Site Formation	33
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	33
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	32
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	32
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	32
SSIF-Affinity: Multimodal Deep Learning of Sequence-Structure Features for Precise Protein–Protein Binding Affinity Prediction	32
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	32
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry	32
Comparative Binding Analysis by Computational Methods and Quartz Crystal Microbalance: Case of hnRNPA2B1 Protein and Irinotecan Drug	32
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	32
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	32
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	32
Rational Design of Single-Phase High-Entropy Oxides via Large Language Model Data Mining and Explainable Machine Learning	31
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	31
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	31
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	31
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	31
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	31
pepADMET: A Novel Computational Platform For Systematic ADMET Evaluation of Peptides	31
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	31
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	31
Mathematical State Function Structure Matters in Metal Oxide Reduction Thermodynamic Modeling	31
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	30
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	30
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	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
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	30
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	30
Issue Publication Information	30
Issue Editorial Masthead	30
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	30
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	30
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	30
Issue Editorial Masthead	30
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	30
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	29
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	29
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design	29
All-Atom Membrane Builder via Multiscale Simulation	29
Issue Editorial Masthead	29
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	29
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	29
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	29
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	29
Correction to “Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond”	29
Uncertainty-Informed Screening for Safer Solvents Used in the Synthesis of Perovskites via Language Models	29
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	29
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	28
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	28
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	28
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	28
Issue Publication Information	28
Enhanced and Classical MD Simulations Map Aggregation-Prone Regions in the Olfactomedin Domain of Myocilin	28
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	28
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	28
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification	28
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	28
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	28
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	28
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	27
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	27
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions	27
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	27
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	27
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	27
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	27
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	27
Preventing AI From Creating Biochemical Threats	27
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	27
PSCG-Net: A Multiscale Crystal Graph Neural Network for Accelerated Materials Discovery	27
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	27
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	26
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	26
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	26
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL	26
AI-Driven Discovery of SARS-CoV-2 Main Protease Fragment-like Inhibitors with Antiviral Activity In Vitro	26
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	26
Traj2Relax: A Trajectory-Supervised Method for Robust Structure Relaxation	26
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	26
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	26
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	26
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	26
MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations	26
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations	26
Ensemble Docking for Intrinsically Disordered Proteins	26