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 2021-05-01 to 2025-05-01.)

Article	Citations
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	3393
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	698
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	525
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach	239
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	195
Lipid Oxidation: Role of Membrane Phase-Separated Domains	175
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling	167
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model	164
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	158
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	147
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	124
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	118
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	116
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	115
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	106
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	103
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	102
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	102
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	97
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	93
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	91
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	90
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	89
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	88
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	86

Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	85
HSQC Spectra Simulation and Matching for Molecular Identification	81
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter	80
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	80
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-	79
Issue Publication Information	79
Issue Publication Information	77
Diffusion Models in De Novo Drug Design	77
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	75
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	71
Large Language Model for Automating the Analysis of Cryoprotectants	69
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	69
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	68
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	68
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	68
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	67
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	66
Issue Publication Information	65
Issue Editorial Masthead	64
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-19	63
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	63
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents	63
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	63
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease	61
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	60
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	60
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials	59
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	59
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	58
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	58
Analysis of Binding Modes of Antigen–Antibody Complexes by Molecular Mechanics Calculation	58
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	57