OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 56. 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 2020-05-01 to 2024-05-01.)

Article	Citations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings	1636
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance	464
ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery	335
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery	187
REINVENT 2.0: An AI Tool for De Novo Drug Design	175
TorchANI: A Free and Open Source PyTorch-Based Deep Learning Implementation of the ANI Neural Network Potentials	150
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects	143
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	137
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction	130
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation	128
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19	128
Rigorous Free Energy Simulations in Virtual Screening	117
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function	115
MolGPT: Molecular Generation Using a Transformer-Decoder Model	114
Assessment of Binding Affinity via Alchemical Free-Energy Calculations	114
SARS-CoV-2 Main Protease: A Molecular Dynamics Study	113
Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease	113
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes	106
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation	106
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation	100
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	100
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design	100
Artificial Intelligence in Chemistry: Current Trends and Future Directions	89
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	88
AmberTools	88

Discovery of New Hydroxyethylamine Analogs against 3CL^pro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies	86
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations	84
Decoding SARS-CoV-2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine	83
MolGpka: A Web Server for Small Molecule pK_a Prediction Using a Graph-Convolutional Neural Network	83
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models	83
Generative Network Complex for the Automated Generation of Drug-like Molecules	81
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)	80
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies	80
iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides	79
PI1M: A Benchmark Database for Polymer Informatics	77
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV-2 Main Protease	76
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta	72
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling	70
Evolution of Alchemical Free Energy Methods in Drug Discovery	70
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature	69
Deep Learning-Based Imbalanced Data Classification for Drug Discovery	68
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro	67
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning	67
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	64
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning	64
Recent Force Field Strategies for Intrinsically Disordered Proteins	64
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M^pro	63
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields	62
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides	62
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations	59
Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations	59
Generative Deep Learning for Targeted Compound Design	59
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate	57
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning	56
De Novo Drug Design of Targeted Chemical Libraries Based on Artificial Intelligence and Pair-Based Multiobjective Optimization	56
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks	56