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 2022-05-01 to 2026-05-01.)

Article	Citations
Issue Publication Information	1742
Recommendations to Improve Text-Based Representation Systems for Polyolefins	466
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	242
MEMO-Stab2: Multi-View Sequence-Based Deep Learning Framework for Predicting Mutation-Induced Stability Changes in Transmembrane Proteins	231
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	212
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	196
Apax: A Flexible and Performant Framework for the Development of Machine-Learned Interatomic Potentials	179
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	166
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	131
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	130
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	130
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	118
DynoPore─A Package to Analyze Molecular Dynamics Trajectories of Confined Liquids	117
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	109
Characterization of Type I/II g-C₃N₄/MoS₂ van der Waals Heterostructures: A New Theoretical Insight	109
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	108
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	107
Enhancing Toxicity Prediction of Synthetic Chemicals via Novel SMILES Fragmentation and Interpretable Deep Learning	106
Chemical Space Exploration and Reinforcement Learning for Discovery of Novel Benzimidazole Hybrid Antibiotics	103
Curating and Visualizing the Analytical Methods and the Open Spectral Database’s Chemical Functional Use Taxonomy	103
Issue Publication Information	99
Issue Publication Information	98
Issue Editorial Masthead	98
Fast, Comprehensive, and User Customizable Macromolecule Interface Analysis with FACE2FACE	96
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	95

Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	90
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	89
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	86
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	78
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	76
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	76
Machine Learning Modeling and Insights into the Structural Characteristics of Drug-Induced Neurotoxicity	74
`KGG` : Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions	73
Hydrogen-Bonding Changes Cause Differences in Imipenem Breakdown Activity in OXA-48 Variants	73
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	72
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	72
ColabReaction: Accelerating Transition State Searches with Machine Learning Potentials on Google Colaboratory	71
QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry	71
Advances and Challenges in De Novo Drug Design Using Three-Dimensional Deep Generative Models	70
From Black Boxes to Actionable Insights: A Perspective on Explainable Artificial Intelligence for Scientific Discovery	70
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	67
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	67
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	66
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	66
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	65
Generative AI Uncovers Novel Chrebp/Txnip Axis Inhibitors with Potential Anti-inflammatory Activity	64
Spatially Resolved Uncertainties for Machine Learning Potentials	63
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	62
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	62
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	62
Identification of New Human P2X7 Antagonists Using Ligand- and Structure-Based Virtual Screening	62
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	61
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	60
Natural Products Repository of Costa Rica (NAPRORE-CR): An Open-Access Database	60
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	60
Diffusion Models in De Novo Drug Design	60
BIOPTIC B1 Ultra-High-Throughput Virtual Screening System Discovers LRRK2 Ligands in Vast Chemical Space	59
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	59
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	59
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	59