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 2021-08-01 to 2025-08-01.)

Article	Citations
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels	947
Pliability in the m⁶A-Binding Region Extends Druggability of YTH Domains	537
Hysteresis Elimination for an Anisotropic Liquid-Crystal Model via Molecule Design and Replica-Exchange Optimization	279
Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models	224
Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket	194
Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis	194
CHARMM36 All-Atom Gas Model for Lipid Nanobubble Simulation	141
Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering	141
Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis	138
HSQC Spectra Simulation and Matching for Molecular Identification	131
Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions	127
Large Language Model for Automating the Analysis of Cryoprotectants	126
Improving Bond Dissociations of Reactive Machine Learning Potentials through Physics-Constrained Data Augmentation	125
Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors	119
Improved Structure-Based Histidine pK_a Prediction for pH-Responsive Protein Design	119
Pore Structure Compartmentalization for Advanced Characterization of Metal–Organic Framework Materials	113
Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis	103
Optimal Compound Downselection To Promote Diversity and Parallel Chemistry	92
Pathfinder─Navigating and Analyzing Chemical Reaction Networks with an Efficient Graph-Based Approach	91
Tree-Invent: A Novel Multipurpose Molecular Generative Model Constrained with a Topological Tree	91
Property-Oriented Reverse Design of Hydrocarbon Fuels Based on c-infoGAN	91
MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design	90
Molecular Dynamics (MD)-Derived Features for Canonical and Noncanonical Amino Acids	85
AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2	83
Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics	81

Spatially Resolved Uncertainties for Machine Learning Potentials	81
Introducing SpaceGA: A Search Tool to Accelerate Large Virtual Screenings of Combinatorial Libraries	78
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease	78
Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR	75
Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR)	75
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site	74
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin	74
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches	74
Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces	73
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method	72
Identification of Potential Aldose Reductase Inhibitors Using Convolutional Neural Network-Based in Silico Screening	72
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	71
Characterization of Type I/II g-C₃N₄/MoS₂ van der Waals Heterostructures: A New Theoretical Insight	71
Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters?	70
Evaluation of Open-Source Large Language Models for Metal–Organic Frameworks Research	69
Natural Language Processing Methods for the Study of Protein–Ligand Interactions	69
Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?	69
Exploring Aromatic Cage Flexibility Using Cosolvent Molecular Dynamics Simulations─An In-Silico Case Study of Tudor Domains	69
Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation	67
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution	63
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography	60
Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site	59
Explainable Graph Neural Networks with Data Augmentation for Predicting pK_a of C–H Acids	57
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses	55
Quantum Descriptors for Predicting and Understanding the Structure–Activity Relationships of Michael Acceptor Warheads	55
Structure–Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda	54
Vina-CUDA: An Efficient Program with in-Depth Utilization of GPU to Accelerate Molecular Docking	54
Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure	54
Mining Knowledge from Crystal Structures: Oxidation States of Oxygen-Coordinated Metal Atoms in Ionic and Coordination Compounds	54
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-	54