Journal of Chemical Information and Modeling

Article	Citations
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design	1377
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	542
Issue Publication Information	355
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	190
Recommendations to Improve Text-Based Representation Systems for Polyolefins	188
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	182
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	153
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	148
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	141
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	124
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	124
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	120
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	109
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	106
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	106
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	105
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	105
Issue Publication Information	100
Issue Editorial Masthead	99
Issue Publication Information	97
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	95
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	93
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	92
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	90
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	89

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	88
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	87
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	86
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	83
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	82
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	79
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	78
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	76
Large Language Model for Automating the Analysis of Cryoprotectants	75
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	72
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	70
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids	70
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	68
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	64
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains	63
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	61
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	61
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	60
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	60
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	59
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	59
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	59
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	58
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	58
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	58
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	57
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	57
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	57
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	57
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	56
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	56
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	55
Characterization of Type I/II g-C3N4/MoS2 van der Waals Heterostructures: A New Theoretical Insight	54
KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	54
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	54
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	54
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	54
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	53
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	52
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	52
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	52
HSQC Spectra Simulation and Matching for Molecular Identification	51
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	51
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	51
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	50
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	50
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	49
Adsorption Energy Prediction Model for CO 2 Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements	49
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	48
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	48

Spatially Resolved Uncertainties for Machine Learning Potentials	48
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	48
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	47
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	47
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	47
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	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
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	46
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	45
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	45
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	45
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	45
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	45
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	45
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	45
Diffusion Models in De Novo Drug Design	44
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	44
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	44
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	43
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	43
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	43
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	43
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	42
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	42
Locating Multiple Transition Pathways for Complex Biomolecules	42
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	42
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	42
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	41
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	41
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	41
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	40
Special Issue on Reaction Informatics and Chemical Space	40
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	40
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	40
af3cli: Streamlining AlphaFold3 Input Preparation	39
Solvation Energetic Costs of Cognate Binding Site Formation	39
Issue Publication Information	39
LISTER: Semiautomatic Metadata Extraction from Annotated Experiment Documentation in eLabFTW	39
Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment	39
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	39
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	38
Modeling Enzyme Temperature Stability from Sequence Segment Perspective	38
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	38
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	38
ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability Prediction	38
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	38
ThermoPred: AI-Enhanced Quantum Chemistry Data Set and ML Toolkit for Thermochemical Properties of API-Like Compounds and Their Degradants	38
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	37
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	37
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	37
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	37
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	37
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	37
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	36
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	36
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	36
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	36
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	36
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	36
EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design	36
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	36
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	35
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	35
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison	35
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	35
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	35
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	34
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	34
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C–H Bonds Catalyzed by the Heterobimetallic Manganese–Iron Hydroxylase AibH1H2 from Rhodococcus	34
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	34
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein	34
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	34
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	33
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	33
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	33
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	33
F-Site: Recognizing Fluorination Patterns in Small-Molecule Drugs via a Two-Stage Transformer-Based Model	33
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	33
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	33
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	33

Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	33
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery	33
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	33
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	32
Knowledge-Based Artificial Intelligence System for Drug Prioritization	32
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	32
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	32
Promiscuity and Quantitative Contribution of UGT2B17 in Drug and Steroid Metabolism Determined by Experimental and Computational Approaches	32
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	32
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	31
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	31
Discovery of P2Y2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening	31
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	31
SSIF-Affinity: Multimodal Deep Learning of Sequence-Structure Features for Precise Protein–Protein Binding Affinity Prediction	31
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	31
Unified Deep Learning Model for Multitask Reaction Predictions with Explanation	31
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	31
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	31
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	31
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	30
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	30
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	30
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	30
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	30
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	30
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	30
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	30
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	30
Issue Publication Information	29
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	29
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	29
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	29
Issue Editorial Masthead	29
Issue Publication Information	29
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations	29
Issue Editorial Masthead	29
Correction to “Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond”	29
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	29
Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis	29
Issue Editorial Masthead	29
NesT-NABind: a Nested Transformer for Nucleic Acid-Binding Site Prediction on Protein Surface	29
Issue Publication Information	29
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	29
High-Throughput Prediction of Metal-Embedded Complex Properties with a New GNN-Based Metal Attention Framework	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
dpdata: A Scalable Python Toolkit for Atomistic Machine Learning Data Sets	28
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	28
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	28
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	28
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	28
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	28
Issue Publication Information	28
All-Atom Membrane Builder via Multiscale Simulation	28
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	28
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	28
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	28
Activity Regulation and Conformation Response of Janus Kinase 3 Mediated by Phosphorylation: Exploration from Correlation Network Analysis and Markov Model	27
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	27
Preventing AI From Creating Biochemical Threats	27
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	27
De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework	27
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	27
Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study	27
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	27
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	27
Uncertainty-Informed Screening for Safer Solvents Used in the Synthesis of Perovskites via Language Models	27
SMICLR: Contrastive Learning on Multiple Molecular Representations for Semisupervised and Unsupervised Representation Learning	27
PSCG-Net: A Multiscale Crystal Graph Neural Network for Accelerated Materials Discovery	26
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine	26
Discovery of a Novel Macrocyclic ATP Citrate Lyase Inhibitor	26
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	26
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	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
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations	26
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	26
Computational Insights into the Regioselective Hydroxylation of Nirmatrelvir Metabolized by Cytochrome P450 3A4	26
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification	26
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets	26
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	25
Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation	25
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	25
HlightReaxMD: A Machine Learning-Augmented Multiscale Analysis Framework for Radiation Chemistry Dynamics and Damage Prediction	25
MPpredictor: An Artificial Intelligence-Driven Web Tool for Composition-Based Material Property Prediction	25
ReactionDataExtractor 2.0: A Deep Learning Approach for Data Extraction from Chemical Reaction Schemes	25
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	25
Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study	25
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations	25
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex	25
Identification of a Cryptic Binding Site in CRISPR-Cas9 for Targeted Inhibition	25
Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM	25
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	25
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	25
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	25
Predicting the Mutagenic Activity of Nitroaromatics Using Conceptual Density Functional Theory Descriptors and Explainable No-Code Machine Learning Approaches	25
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	24