OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 54. 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 2021-11-01 to 2025-11-01.)

Article	Citations
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	1191
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	540
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	308
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	167
Issue Publication Information	163
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	163
Recommendations to Improve Text-Based Representation Systems for Polyolefins	139
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	139
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	134
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	121
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	113
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	105
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	103
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	103
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	101
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	100
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	97
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	93
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	91
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	91
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	88
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	87
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	87
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	86
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	84

Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	84
Diffusion Models in De Novo Drug Design	84
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	80
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	79
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	78
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	77
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	77
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	76
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	75
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	75
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	69
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	69
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	64
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	61
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	61
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	59
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	59
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	59
Issue Publication Information	57
Issue Publication Information	57
Issue Editorial Masthead	57
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	56
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	56
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	55
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	54
`KGG`: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	54
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	54
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	54
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	54