Journal of Chemical Information and Modeling

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.)
ArticleCitations
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds3393
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels698
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors525
Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach239
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution195
Lipid Oxidation: Role of Membrane Phase-Separated Domains175
Improved Prediction of Ligand–Protein Binding Affinities by Meta-modeling167
ProtChat: An AI Multi-Agent for Automated Protein Analysis Leveraging GPT-4 and Protein Language Model164
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)158
Pliability in the m6A-Binding Region Extends Druggability of YTH Domains147
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization124
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion118
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models116
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design115
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction106
Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C–H Acids103
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications102
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis102
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins97
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method93
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket91
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree90
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering89
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation88
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder86
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis85
HSQC Spectra Simulation and Matching for Molecular Identification81
Boosting the Accuracy and Chemical Space Coverage of the Detection of Small Colloidal Aggregating Molecules Using the BAD Molecule Filter80
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening80
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 Information79
Issue Publication Information77
Diffusion Models in De Novo Drug Design77
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-1975
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions71
Large Language Model for Automating the Analysis of Cryoprotectants69
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation69
Improved Structure-Based Histidine pKa Prediction for pH-Responsive Protein Design68
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design68
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda68
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site67
Natural Language Processing Methods for the Study of Protein–Ligand Interactions66
Issue Publication Information65
Issue Editorial Masthead64
Knowledge Graph-Based Approaches to Drug Repurposing for COVID-1963
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure63
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents63
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 Protease61
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-260
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin60
DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials59
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding59
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains58
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads58
Analysis of Binding Modes of Antigen–Antibody Complexes by Molecular Mechanics Calculation58
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography57
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