OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 56. 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 2022-01-01 to 2026-01-01.)

Article	Citations
Improved Structure-Based Histidine pK_a 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
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	105
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	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 pK_a 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
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	58
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
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	57
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
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