OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Chemical Information and Modeling is 3. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-04-01 to 2026-04-01.)

Article	Citations
Issue Publication Information	1652
Recommendations to Improve Text-Based Representation Systems for Polyolefins	437
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	237
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	221
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	201
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	185
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	170
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	153
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	128
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	128
Issue Publication Information	125
Issue Editorial Masthead	125
Issue Publication Information	116
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	111
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	107
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	107
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	105
Adsorption Energy Prediction Model for CO ₂ Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements	104
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	103
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	102
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	100
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	96
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	96
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	94
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	94

HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	93
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	88
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	86
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	86
Large Language Model for Automating the Analysis of Cryoprotectants	84
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	78
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	75
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	73
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	72
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	70
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	70
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	70
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	68
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	68
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	67
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	67
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	66
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	65
HSQC Spectra Simulation and Matching for Molecular Identification	65
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	64
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	64
`KGG` : Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	63
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	63
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	61
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	61
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	60
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	60
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	59
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	59
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	59
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	59
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	59
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids	58
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	58
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	58
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	57
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	57
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	56
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	56
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	56
Spatially Resolved Uncertainties for Machine Learning Potentials	53
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	53
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	53
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	52
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	52
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	52
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	52
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	51
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	51
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	51

QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	50
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	50
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	49
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	49
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	49
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	49
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	49
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	48
MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation	48
Generative AI Uncovers Novel Chrebp/Txnip Axis Inhibitors with Potential Anti-inflammatory Activity	48
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	48
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	46
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	45
Characterization of Type I/II g-C₃N₄/MoS₂ van der Waals Heterostructures: A New Theoretical Insight	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
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	45
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	45
EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation	45
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	45
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	45
Diffusion Models in De Novo Drug Design	44
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	44
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	43
Locating Multiple Transition Pathways for Complex Biomolecules	43
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	43
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening	43
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	43
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	43
af3cli: Streamlining AlphaFold3 Input Preparation	42
Atomic-Level View of the Functional Transition in Vertebrate Hemoglobins: The Case of Antarctic Fish Hbs	42
Exploring Drug Repurposing for Influenza A (H3N2) Virus: A Computational Approach to Identifying Commercialized Drugs Targeting Hemagglutinin, Neuraminidase, and Nucleoprotein	42
Issue Publication Information	42
The Use of Glycan Ensemble Structures and Nonpolar Surface Area Distributions for Correlating with Liquid Chromatography Retention Times	42
PPDock: Pocket Prediction-Based Protein–Ligand Blind Docking	42
Special Issue on Reaction Informatics and Chemical Space	42
Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction	41
Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries	41
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets	41
Fuzz Testing Molecular Representation Using Deep Variational Anomaly Generation	41
Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments	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
Molecular Determinants of EphA2 and EphB2 Antagonism Enable the Design of Ligands with Improved Selectivity	40
Recognition Mechanisms between a Nanobody and Disordered Epitopes of the Human Prion Protein: An Integrative Molecular Dynamics Study	39
Can Focusing on One Deep Learning Architecture Improve Fault Diagnosis Performance?	39
Correction to “Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers”	39
Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms	39
Computational Exploration of the Inhibitory Mechanism of mRNA against the Phase Separation of hnRNPA2 Low Complexity Domains	39
SDBA: Score Domain-Based Attention for DNA N4-Methylcytosine Site Prediction from Multiperspectives	39
A Catalytic Perspective on Erythromycin Hydrolysis by Erythromycin Esterase C: Combined CpHMD and QM/MM Metadynamics Study	38
Modeling Enzyme Temperature Stability from Sequence Segment Perspective	38
PMODiff: Physics-Informed Multi-Objective Optimization Diffusion Model for Protein-Specific 3D Molecule Generation	38
Hybrid Machine Learning and Experimental Studies of Antiviral Potential of Ionic Liquids against P100, MS2, and Phi6	37
Deciphering Binding Site Conformational Variability of Substrate Promiscuous and Specialist Enzymes	37
Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study	37
Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids	37
PymolFold: A PyMOL Plugin for API-Driven Structure Prediction and Quality Assessment	37
PolyConstruct: Adapting Biomolecular Simulation Pipelines for Polymers with PolyBuild, PolyConf, and PolyTop	36
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery	36
Mechanistic Insights into the Dioxygen Activation and Hydroxylation of Aliphatic C–H Bonds Catalyzed by the Heterobimetallic Manganese–Iron Hydroxylase AibH1H2 from Rhodococcus	36
F-Site: Recognizing Fluorination Patterns in Small-Molecule Drugs via a Two-Stage Transformer-Based Model	36
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors	36
Systematic Search for Blood–Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain–Domain Docking	36
Predicting the Likelihood of Molecules to Act as Modulators of Protein–Protein Interactions	35
Interaction of Radiopharmaceuticals with Somatostatin Receptor 2 Revealed by Molecular Dynamics Simulations	35
Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands	35
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery	35
Knowledge-Based Artificial Intelligence System for Drug Prioritization	35
On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction	35
ProfhEX: Empowering Early Drug Discovery with Machine Learning-Based Target Profiling and Liability Prediction	34
Augmented Reality, a Review of a Way to Represent and Manipulate 3D Chemical Structures	34
Catalyst Design and Feature Engineering to Improve Selectivity and Reactivity in Two Simultaneous Cross-Coupling Reactions	34
EDWARD: E(3)-Equivariant Dual-Way Attentive Reduction for Peptide-to-Small-Molecule Design	34
ESPDHot: An Effective Machine Learning-Based Approach for Predicting Protein–DNA Interaction Hotspots	34
Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers	34
Immobilization of Cellulase Enzymes on Single-Walled Carbon Nanotubes for Recycling of Enzymes and Better Yield of Bioethanol Using Computer Simulations	34
ThermoPred: AI-Enhanced Quantum Chemistry Data Set and ML Toolkit for Thermochemical Properties of API-Like Compounds and Their Degradants	34
Solvation Energetic Costs of Cognate Binding Site Formation	33
Computational Study of Heme b ₅₉₅ to Heme d Electron Transfer in	33
Scoring Conformational Metastability of Macrocyclic Peptides with Binding Pose Metadynamics	33

CompBind: Complex Guided Pretraining-Based Structure-Free Protein–Ligand Affinity Prediction	33
Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design	33
Hybrid Diffusion Model for Stable, Affinity-Driven, Receptor-Aware Peptide Generation	33
AI-Guided Conformational Dynamics of p53 L1 Loop Reveal an Allosteric Switch Regulating DNA Binding and Cancer Hotspots	33
Sequential Contrastive and Deep Learning Models to Identify Selective Butyrylcholinesterase Inhibitors	32
Can Reasoning Power Significantly Improve the Knowledge of Large Language Models for Chemistry?─Based on Conversations with LLMs	32
SSIF-Affinity: Multimodal Deep Learning of Sequence-Structure Features for Precise Protein–Protein Binding Affinity Prediction	32
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement	32
Evaluation of AlphaFold2 Structures for Hit Identification across Multiple Scenarios	32
DFRscore: Deep Learning-Based Scoring of Synthetic Complexity with Drug-Focused Retrosynthetic Analysis for High-Throughput Virtual Screening	32
De Novo Drug Design Using Reinforcement Learning with Graph-Based Deep Generative Models	32
Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA–Drug Associations	32
RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA–Protein Interaction Prediction	32
Identification of New Carbonic Anhydrase VII Inhibitors by Structure-Based Virtual Screening	31
E46K Mutation of α-Synuclein Preorganizes the Intramolecular Interactions Crucial for Aggregation	31
molSimplify 2.0: Improved Structure Generation for Automating Discovery in Inorganic Molecular and Reticular Chemistry	31
ncProFormer: A CNN-enhanced Transformer for ncRNA Coding-Potential Prediction	31
Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?	31
Interpreting Neural Network Models for Toxicity Prediction by Extracting Learned Chemical Features	31
A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions	31
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations	31
PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs	31
Comparative Binding Analysis by Computational Methods and Quartz Crystal Microbalance: Case of hnRNPA2B1 Protein and Irinotecan Drug	31
Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes	31
Recent Advances in the Modeling of Ionic Liquids Using Artificial Neural Networks	31
KnoMol: A Knowledge-Enhanced Graph Transformer for Molecular Property Prediction	31
OpticalBERT and OpticalTable-SQA: Text- and Table-Based Language Models for the Optical-Materials Domain	30
EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing	30
pepADMET: A Novel Computational Platform For Systematic ADMET Evaluation of Peptides	30
Issue Editorial Masthead	30
RLSynC: Offline–Online Reinforcement Learning for Synthon Completion	30
TIRESIA: An eXplainable Artificial Intelligence Platform for Predicting Developmental Toxicity	30
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes	30
MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction	30
Issue Publication Information	30
ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities	30
HergSPred: Accurate Classification of hERG Blockers/Nonblockers with Machine-Learning Models	30
BNM-CDGNN: Batch Normalization Multilayer Perceptron Crystal Distance Graph Neural Network for Excellent-Performance Crystal Property Prediction	30
Issue Publication Information	30
Energy-Guided Denoising Contrastive Learning for Molecular Property Prediction	30
Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C	29
BEMM-GEN: A Toolkit for Generating a Biomolecular Environment-Mimicking Model for Molecular Dynamics Simulation	29
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures	29
Issue Editorial Masthead	29
Mask-Guided Target Node Feature Learning and Dynamic Detailed Feature Enhancement for lncRNA-Disease Association Prediction	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
TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms	29
Issue Editorial Masthead	29
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1	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
Bound Phospholipids Assist Cholesteryl Ester Transfer in the Cholesteryl Ester Transfer Protein	28
Transcriptionally Conditional Recurrent Neural Network for De Novo Drug Design	28
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies	28
Novel Dimeric hHv1 Model and Structural Bioinformatic Analysis Reveal an ATP-Binding Site Resulting in a Channel Activating Effect	28
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	28
Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus	28
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design	28
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces	28
Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis	28
MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning	28
Performance Analysis of CP2K Code for Ab Initio Molecular Dynamics on CPUs and GPUs	27
Activation and Reactivity of the Deubiquitinylase OTU Cezanne-2 from MD Simulations and QM/MM Calculations	27
KUTE: Green–Kubo Uncertainty-Based Transport Coefficient Estimator	27
Transformer Performance for Chemical Reactions: Analysis of Different Predictive and Evaluation Scenarios	27
Incorporating Neighboring Protein Features for Enhanced Drug–Target Interaction Prediction: A Comparative Analysis of Similarity-Based Alignment Methods	27
dpdata: A Scalable Python Toolkit for Atomistic Machine Learning Data Sets	27
All-Atom Membrane Builder via Multiscale Simulation	27
SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges	27
Issue Publication Information	27
Computational Insights into the Regioselective Hydroxylation of Nirmatrelvir Metabolized by Cytochrome P450 3A4	27
ACGCN: Graph Convolutional Networks for Activity Cliff Prediction between Matched Molecular Pairs	27
Multimillion Atom Simulations of Di-8-ANEPPS Chromophores Embedded in a Model Plasma Membrane: Toward the Investigation of Realistic Dyed Cell Membranes	27
Integrative Computational Analysis of Common EXO5 Haplotypes: Impact on Protein Dynamics, Genome Stability, and Cancer Progression	27
Equivariant Graph-Representation-Based Actor–Critic Reinforcement Learning for Nanoparticle Design	27
Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification	27
Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs	27
Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort	27
Enhanced and Classical MD Simulations Map Aggregation-Prone Regions in the Olfactomedin Domain of Myocilin	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
PSCG-Net: A Multiscale Crystal Graph Neural Network for Accelerated Materials Discovery	26
Preventing AI From Creating Biochemical Threats	26
Autobench V1.0: Benchmarking Automation for Electronic Structure Calculations	26
Large-Scale Modeling of Sparse Protein Kinase Activity Data	26
Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets	26
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions	26
Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach	26
Size Matters: A Computational Study of Hydrogen Absorption in Ionic Liquids	26
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents	26
All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System	26
Determining Lennard-Jones Parameters Using Multiscale Target Data through Presampling-Enhanced, Surrogate-Assisted Global Optimization	26
CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides	26
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study	26
EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit	26
Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin	26