OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 58. 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 2020-03-01 to 2024-03-01.)

Article	Citations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings	1406
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance	449
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study	328
ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery	308
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery	174
REINVENT 2.0: An AI Tool for De Novo Drug Design	160
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations	151
The Synthesizability of Molecules Proposed by Generative Models	143
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials	139
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects	137
Deep Dive into Machine Learning Models for Protein Engineering	130
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	130
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction	125
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19	124
Deep Generative Models for 3D Linker Design	120
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease	112
Rigorous Free Energy Simulations in Virtual Screening	112
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation	112
Evaluating Scalable Uncertainty Estimation Methods for Deep Learning-Based Molecular Property Prediction	111
Assessment of Binding Affinity via Alchemical Free-Energy Calculations	110
SARS-CoV-2 Main Protease: A Molecular Dynamics Study	108
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes	103
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function	103
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation	97
MolGPT: Molecular Generation Using a Transformer-Decoder Model	96

Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design	95
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation	94
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	90
LIT-PCBA: An Unbiased Data Set for Machine Learning and Virtual Screening	89
Discovery of New Hydroxyethylamine Analogs against 3CL^pro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies	85
Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis	83
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine	82
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations	82
Artificial Intelligence in Chemistry: Current Trends and Future Directions	81
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)	80
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models	80
Generative Network Complex for the Automated Generation of Drug-like Molecules	79
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences	78
MolGpka: A Web Server for Small Molecule pK_a Prediction Using a Graph-Convolutional Neural Network	77
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies	75
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease	74
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides	72
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling	70
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta	70
PI1M: A Benchmark Database for Polymer Informatics	67
Evolution of Alchemical Free Energy Methods in Drug Discovery	66
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro	65
Deep Learning-Based Imbalanced Data Classification for Drug Discovery	64
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning	62
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning	62
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M^pro	61
Recent Force Field Strategies for Intrinsically Disordered Proteins	61
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields	61
Rapid Identification of X-ray Diffraction Patterns Based on Very Limited Data by Interpretable Convolutional Neural Networks	60
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	59
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides	58
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature	58
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations	58