OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 59. 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 2022-08-01 to 2026-08-01.)

Article	Citations
Issue Publication Information	2036
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	568
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	289
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	279
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	246
Issue Publication Information	211
Issue Editorial Masthead	194
Issue Publication Information	188
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	159
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	152
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	146
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	135
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	135
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	126
State Ensemble Energy Recognition (SEER): A Hybrid Gas-Phase Molecular Charge State Predictor	125
HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug–Target Interaction Prediction	125
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	124
EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation	116
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models	113
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	108
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	108
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	105
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	104
Efficient Characterization of GPCRs Allosteric Modulation: Application to the Rational Design of De Novo S1PR1 Allosteric Modulators	103
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	94

Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	94
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	91
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	89
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	87
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	86
A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations	83
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	83
MEHC-Curation: A Python Framework for High-Quality Molecular Data Set Curation	81
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	80
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	80
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	79
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	78
Spatially Resolved Uncertainties for Machine Learning Potentials	78
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	77
Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants	77
Recommendations to Improve Text-Based Representation Systems for Polyolefins	73
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	71
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids	71
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	69
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	67
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	66
eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems	65
Assessment of Alphafold Protein Models for Small-Molecule Ligand Docking versus Co-Folding	64
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	64
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	63
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	63
Band Gap and Reorganization Energy Prediction of Conducting Polymers by the Integration of Machine Learning and Density Functional Theory	62
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	61
Large Language Model for Automating the Analysis of Cryoprotectants	61
HSQC Spectra Simulation and Matching for Molecular Identification	61
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	61
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	61
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	61
Accurate Simulations of Water and Aqueous Solutions through Fine-Tuned Dispersion-Corrected Density Functional Theory and Machine-Learning Interatomic Potentials	61
ESM2-BiMamba: A Length-Adaptive Hybrid Framework for Efficient Concurrent Prediction of DNA-Binding Proteins and DNA-Binding Residue Sites	59
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	59