OOIR: Observatory of International Research

Papers

(The H4-Index of Journal of Chemical Information and Modeling is 53. 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 2020-11-01 to 2024-11-01.)

Article	Citations
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings	2270
Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance	491
AmberTools	270
Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference	161
MolGPT: Molecular Generation Using a Transformer-Decoder Model	160
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation	155
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function	139
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19	135
Machine Learning Meets with Metal Organic Frameworks for Gas Storage and Separation	128
Systematic Comparison of the Structural and Dynamic Properties of Commonly Used Water Models for Molecular Dynamics Simulations	120
Artificial Intelligence in Chemistry: Current Trends and Future Directions	119
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models	109
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation	105
MolGpka: A Web Server for Small Molecule pK_a Prediction Using a Graph-Convolutional Neural Network	102
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	101
Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations	88
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta	85
Benchmarking Machine Learning Models for Polymer Informatics: An Example of Glass Transition Temperature	84
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning	83
Group Contribution and Machine Learning Approaches to Predict Abraham Solute Parameters, Solvation Free Energy, and Solvation Enthalpy	81
Chemprop: A Machine Learning Package for Chemical Property Prediction	80
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides	77
Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations	76
Recent Force Field Strategies for Intrinsically Disordered Proteins	76
Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling	75

Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro	71
Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields	71
Generative Deep Learning for Targeted Compound Design	71
Transferable Multilevel Attention Neural Network for Accurate Prediction of Quantum Chemistry Properties via Multitask Learning	69
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate	68
Exposing the Limitations of Molecular Machine Learning with Activity Cliffs	68
Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations	67
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits	66
BBPpred: Sequence-Based Prediction of Blood-Brain Barrier Peptides with Feature Representation Learning and Logistic Regression	65
Exploration of Ultralarge Compound Collections for Drug Discovery	63
Quantum Machine Learning Algorithms for Drug Discovery Applications	63
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor	63
Identifying SNARE Proteins Using an Alignment-Free Method Based on Multiscan Convolutional Neural Network and PSSM Profiles	62
Computational Methods and Tools in Antimicrobial Peptide Research	61
SMILES to Smell: Decoding the Structure–Odor Relationship of Chemical Compounds Using the Deep Neural Network Approach	60
Accelerating De Novo Drug Design against Novel Proteins Using Deep Learning	59
ChemDataExtractor 2.0: Autopopulated Ontologies for Materials Science	59
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction	59
Program Package for the Calculation of Origin-Independent Electron Current Density and Derived Magnetic Properties in Molecular Systems	58
ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery	58
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 M^pro	58
tmQM Dataset—Quantum Geometries and Properties of 86k Transition Metal Complexes	58
Property-Unmatched Decoys in Docking Benchmarks	57
N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study	56
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro	56
Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations	55
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design	54
RMG Database for Chemical Property Prediction	54
xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning	53