OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 57. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	3582
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	784
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	528
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	249
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	182
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	181
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	171
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	170
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	153
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	127
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	124
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	122
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	118
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	117
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	111
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	110
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	107
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	106
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	104
HSQC Spectra Simulation and Matching for Molecular Identification	101
Issue Publication Information	98
Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19	97
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	92
Large Language Model for Automating the Analysis of Cryoprotectants	86
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	84

Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	83
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	82
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	82
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	82
Issue Editorial Masthead	81
Issue Publication Information	81
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	78
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	76
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	75
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	74
Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder	72
Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis	70
Spatially Resolved Uncertainties for Machine Learning Potentials	70
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	69
Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)	68
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	66
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	66
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	66
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	64
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	64
FEP Augmentation as a Means to Solve Data Paucity Problems for Machine Learning in Chemical Biology	64
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	64
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	63
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	63
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	62
The Often-Overlooked Power of Summary Statistics in Exploratory Data Analysis: Comparison of Pattern Recognition Entropy (PRE) to Other Summary Statistics and Introduction of Divided Spectrum-PRE (DS-	61
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	61
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	60
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	60
Bioactive Natural Products Identification Using Automation of Molecular Networking Software	59
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	57
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	57
Cyclosporin A: Conformational Complexity and Chameleonicity	57