OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 58. 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 2022-06-01 to 2026-06-01.)

Article	Citations
Issue Publication Information	1820
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	490
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	255
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	243
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	216
Issue Publication Information	205
Issue Editorial Masthead	183
Issue Publication Information	170
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	135
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	133
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	131
Adsorption Energy Prediction Model for CO ₂ Reduction on Electrocatalysts Containing Previously Unencountered Metal Elements	123
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	120
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	112
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	109
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	108
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	107
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	106
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	106
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	105
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	104
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	102
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	99
EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation	98
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	93

Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	92
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	91
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	88
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	82
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	79
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	78
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	78
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	75
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	75
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	75
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	75
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	74
Generative AI Uncovers Novel Chrebp/Txnip Axis Inhibitors with Potential Anti-inflammatory Activity	74
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	73
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	69
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	68
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	68
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	67
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	66
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	66
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	65
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	63
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	63
Characterization of Type I/II g-C₃N₄/MoS₂ van der Waals Heterostructures: A New Theoretical Insight	63
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	63
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	63
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	63
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	62
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	62
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	60
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	60
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	59
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	58
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	58
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	58