Journal of Chemical Information and Modeling

Article	Citations
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	1280
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	541
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	334
Issue Publication Information	178
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	176
Recommendations to Improve Text-Based Representation Systems for Polyolefins	174
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	146
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	145
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	141
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	122
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	118
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	113
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	109
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	105
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	103
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	101
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	95
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	95
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	94
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	93
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	90
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	90
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	89
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	89
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	85

Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	85
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	85
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	82
Issue Publication Information	81
Issue Editorial Masthead	80
Issue Publication Information	79
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	78
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	76
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	73
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	71
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	70
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	65
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	63
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	61
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	61
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	60
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	59
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	59
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	58
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	58
Large Language Model for Automating the Analysis of Cryoprotectants	57
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	57
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	57
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	57
Spatially Resolved Uncertainties for Machine Learning Potentials	56
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	56
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	56
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	55
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	55
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	55
KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	54
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	54
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	53
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	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
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	52
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	52
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	51
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	51
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	51
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	51
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	50
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	49
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	49
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	48
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	48
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	48
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	48
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	47
HSQC Spectra Simulation and Matching for Molecular Identification	47

Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	47
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	46
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	45
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	45
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	45
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	44
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	44
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	44
Diffusion Models in De Novo Drug Design	44
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	44
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	43
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	43
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	43
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	43
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	43
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	43
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	43
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	43
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	42
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	42
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	42
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	41
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	41
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	41
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	40
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	40
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	40
Locating Multiple Transition Pathways for Complex Biomolecules	40
af3cli: Streamlining AlphaFold3 Input Preparation	39
Special Issue on Reaction Informatics and Chemical Space	39
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	39
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	39
Issue Publication Information	39
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	39
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	39
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	39
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	39
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	39
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	38
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	38
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	38
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	38
Solvation Energetic Costs of Cognate Binding Site Formation	38
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	38
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	37
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	37
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	37
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	37
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	37
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	36
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	36
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	36
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	36
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	36
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	36
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	36
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	35
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	35
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	35
Atomic Polarizabilities for Interactive Dipole Induction Models	35
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	35
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	35
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	35
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C–H Bonds Catalyzed by the Heterobimetallic Manganese–Iron Hydroxylase AibH1H2 from Rhodococcus	35
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	35
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein	35
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	35
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	34
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	34
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	34
Knowledge-Based Artificial Intelligence System for Drug Prioritization	33
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	33
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	33
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	33
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	33
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	33
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	33
Modeling Enzyme Temperature Stability from Sequence Segment Perspective	33
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	33
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	33

OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	33
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	32
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	32
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery	32
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	32
F-Site: Recognizing Fluorination Patterns in Small-Molecule Drugs via a Two-Stage Transformer-Based Model	32
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	31
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	31
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	31
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	31
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	31
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	31
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	31
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	31
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	31
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	31
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	31
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	30
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	30
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	30
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	30
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	30
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	30
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	30
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	30
Issue Publication Information	29
Issue Editorial Masthead	29
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	29
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	29
Issue Publication Information	29
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	29
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	29
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	29
Issue Publication Information	29
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	29
Issue Editorial Masthead	29
Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis	28
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking	28
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	28
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	28
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	28
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	28
Uncertainty-Informed Screening for Safer Solvents Used in the Synthesis of Perovskites via Language Models	28
Issue Editorial Masthead	28
Correction to “Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond”	28
dpdata: A Scalable Python Toolkit for Atomistic Machine Learning Data Sets	28
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	28
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	28
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations	28
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	27
All-Atom Membrane Builder via Multiscale Simulation	27
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein	27
Issue Publication Information	27
Preventing AI From Creating Biochemical Threats	27
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	27
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	27
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	27
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	27
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	27
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	27
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	27
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	27
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	27
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	27
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	26
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction	26
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	26
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	26
PSCG-Net: A Multiscale Crystal Graph Neural Network for Accelerated Materials Discovery	26
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	26
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	26
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	26
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
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	26
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	26
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	26
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity	26
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	26
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification	26
Fast Prediction of Lipophilicity of Organofluorine Molecules: Deep Learning-Derived Polarity Characters and Experimental Tests	25
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	25
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	25
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	25
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	25
Ring Repeating Unit: An Upgraded Structure Representation of Linear Condensation Polymers for Property Prediction	25
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	25
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	25
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	25
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	25
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework	24
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	24
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	24
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study	24
HlightReaxMD: A Machine Learning-Augmented Multiscale Analysis Framework for Radiation Chemistry Dynamics and Damage Prediction	24
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	24