OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 52. 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 2021-02-01 to 2025-02-01.)

Article	Citations
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors	2664
Comprehensive Evaluation of 10 Docking Programs on a Diverse Set of Protein–Cyclic Peptide Complexes	504
Computational Study of Driving Forces in ATSP, PDIQ, and P53 Peptide Binding: C═O···C═O Tetrel Bonding Interactions at Work	404
Role of Stacking Interactions in the Stability of Primitive Genetics: A Quantum Chemical View	175
Issue Editorial Masthead	173
ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation	161
An Automated Approach for Domain-Specific Knowledge Graph Generation─Graph Measures and Characterization	147
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	131
DO-GMA: An End-to-End Drug–Target Interaction Identification Framework with a Depthwise Overparameterized Convolutional Network and the Gated Multihead Attention Mechanism	129
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	127
Comparative Analysis of Recurrent Neural Networks with Conjoint Fingerprints for Skin Corrosion Prediction	122
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations	115
ComNet: A Multiview Deep Learning Model for Predicting Drug Combination Side Effects	112
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models	106
Peptide-Aware Chemical Language Model Successfully Predicts Membrane Diffusion of Cyclic Peptides	95
Active Learning to Select the Most Suitable Reagents and One-Step Organic Chemistry Reactions for Prioritizing Target-Specific Hits from Ultralarge Chemical Spaces	92
DENVIS: Scalable and High-Throughput Virtual Screening Using Graph Neural Networks with Atomic and Surface Protein Pocket Features	92
Exploring the pH- and Ligand-Dependent Flap Dynamics of Malarial Plasmepsin II	84
Evaluating Machine Learning Methods of Analyzing Multiclass Metabolomics	83
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	83
Hotspot Identification and Drug Design of Protein–Protein Interaction Modulators Using the Fragment Molecular Orbital Method	78
Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein–Ligand Binding Affinity Prediction	76
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	76
Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development	75
Classification Model for the Second Extracellular Loop of Class A GPCRs	75

Simulated Drug Efflux for the AbgT Family of Membrane Transporters	75
All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric Peptide	72
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design	71
Dynamics and Allosteric Information Pathways of Unphosphorylated c-Cbl	71
Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ^ANdG- and ^APdG-Containing DNA Duplexes	69
Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors?	67
Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States	66
Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach	66
Data-Driven Prediction of Configurational Stability of Molecule-Adsorbed Heterogeneous Catalysts	65
Issue Editorial Masthead	64
De Novo Transmembrane Aggregation of Aβ10–40 Peptides in an Anionic Lipid Bilayer	64
Issue Editorial Masthead	63
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences	63
Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors	63
Issue Publication Information	61
Pynta─An Automated Workflow for Calculation of Surface and Gas–Surface Kinetics	59
ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures	59
PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands	58
Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations	58
Issue Publication Information	58
Selective Inhibitor Design for Kinase Homologs Using Multiobjective Monte Carlo Tree Search	56
Automated Adsorption Workflow for Semiconductor Surfaces and the Application to Zinc Telluride	56
Mebendazole’s Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90	56
Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum	55
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	55
Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening	54
On Quality Thresholds for the Clustering of Molecular Structures	52
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach	52
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	52