OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 54. 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 2021-09-01 to 2025-09-01.)

Article	Citations
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	1028
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	540
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	294
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	250
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	200
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	150
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	146
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	144
HSQC Spectra Simulation and Matching for Molecular Identification	135
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	131
Large Language Model for Automating the Analysis of Cryoprotectants	127
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	126
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	120
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	114
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	107
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	98
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	97
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	94
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	94
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	91
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	89
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	89
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	84
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	82
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	81

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	81
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	79
Characterization of Type I/II g-C₃N₄/MoS₂ van der Waals Heterostructures: A New Theoretical Insight	78
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	77
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	77
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	76
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site	76
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	74
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-	73
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	73
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	73
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	73
SSIPTools: Software and Methodology for Surface Site Interaction Point (SSIP) Approach and Applications	72
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	72
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	72
TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion	71
Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans	71
Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs	63
Gex2SGen: Designing Drug-like Molecules from Desired Gene Expression Signatures	59
De Novo Design of Molecules with Multiaction Potential from Differential Gene Expression using Variational Autoencoder	59
E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding	57
Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits	57
Issue Publication Information	56
Issue Editorial Masthead	56
Issue Publication Information	56
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction	55
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins	55
Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants”	54
Cyclosporin A: Conformational Complexity and Chameleonicity	54