Journal of Chemical Information and Modeling

Article	Citations
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	1095
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	540
HSQC Spectra Simulation and Matching for Molecular Identification	314
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	276
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	162
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	160
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	157
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	150
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	133
Issue Publication Information	133
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	132
Recommendations to Improve Text-Based Representation Systems for Polyolefins	122
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	119
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	111
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	100
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	99
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	98
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	96
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	96
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	94
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	87
Spatially Resolved Uncertainties for Machine Learning Potentials	85
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	85
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	84
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	84

De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	82
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	82
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	81
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	80
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	80
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	79
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	78
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	76
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	76
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	74
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	74
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	73
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	73
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	69
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	66
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	63
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	62
Issue Publication Information	60
Issue Editorial Masthead	59
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	58
Issue Publication Information	58
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	57
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	57
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	56
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	56
KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	55
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	54
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	53
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	53
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	53
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	53
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	53
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	52
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	51
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	51
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	50
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	50
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	50
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	49
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	49
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	49
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	48
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	48
Large Language Model for Automating the Analysis of Cryoprotectants	48
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	47
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	47
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	47
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	46
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	46
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	46

Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	46
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	45
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	45
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	45
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	45
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	44
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	44
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	43
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	43
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	43
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	43
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	43
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	43
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	42
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	42
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	42
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	42
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	42
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	42
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	41
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	41
Diffusion Models in De Novo Drug Design	40
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	40
Cyclosporin A: Conformational Complexity and Chameleonicity	40
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	39
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	39
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	39
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	39
Locating Multiple Transition Pathways for Complex Biomolecules	39
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	38
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	38
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	38
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	38
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	38
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	38
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	38
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	37
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	37
Special Issue on Reaction Informatics and Chemical Space	37
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	37
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	37
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	37
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	37
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations	36
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	36
Issue Publication Information	36
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	36
af3cli: Streamlining AlphaFold3 Input Preparation	36
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	36
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	36
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	35
Solvation Energetic Costs of Cognate Binding Site Formation	35
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	35
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	35
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	35
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	34
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	34
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	34
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	34
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	34
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	34
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	33
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	33
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	33
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	33
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	33
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	33
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	32
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	32
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	32
Knowledge-Based Artificial Intelligence System for Drug Prioritization	32
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	32
First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach	32
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	32
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	32
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	32
Automated Construction of Neural Network Potential Energy Surface: The Enhanced Self-Organizing Incremental Neural Network Deep Potential Method	31
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	31
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	31
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	31

Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	31
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	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	31
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	31
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	30
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	30
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	30
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	30
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	30
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	30
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	30
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	30
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	30
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	30
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	30
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	29
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	29
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	29
Atomic Polarizabilities for Interactive Dipole Induction Models	29
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	29
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	29
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	29
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	29
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	28
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	28
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	28
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	28
Issue Publication Information	28
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	28
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	28
Issue Editorial Masthead	28
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	28
Issue Publication Information	27
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	27
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	27
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	27
Issue Publication Information	27
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	27
Discovery of New Estrogen-Related Receptor α Agonists via a Combination Strategy Based on Shape Screening and Ensemble Docking	27
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	27
Preventing AI From Creating Biochemical Threats	27
Issue Editorial Masthead	27
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	27
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	27
Large Language Models as Tools for Molecular Toxicity Prediction: AI Insights into Cardiotoxicity	27
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	26
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	26
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	26
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	26
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	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
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
Uncertainty-Informed Screening for Safer Solvents Used in the Synthesis of Perovskites via Language Models	26
Gaussian Process Approach to Constructing Transferable Force Fields for Thiolate-Protected Gold Nanoclusters	26
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	26
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	26
Ensemble Docking for Intrinsically Disordered Proteins	26
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	26
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	26
TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms	26
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	25
Modeling the Structure–Activity Relationship of Arbidol Derivatives and Other SARS-CoV-2 Fusion Inhibitors Targeting the S2 Segment of the Spike Protein	25
Issue Publication Information	25
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	25
Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes	25
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	25
Large-Scale Modeling of Sparse Protein Kinase Activity Data	25
Large-Scale Distributed Training of Transformers for Chemical Fingerprinting	25
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	25
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction	24
Hit Identification Driven by Combining Artificial Intelligence and Computational Chemistry Methods: A PI5P4K-β Case Study	24
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	24
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	24
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets	24
All-Atom Membrane Builder via Multiscale Simulation	24
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	24
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	24
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	24
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	24
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	24
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	24
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus	24
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	24
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	24
OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions	24
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	24
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	24
Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor	24
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	24
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	24
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework	24
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	23
Cluster Analysis in Liquids: A Novel Tool in TRAVIS	23