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Multi-Step Protocol for Automatic Evaluation of Docking Results Based on Machine Learning Methods—A Case Study of Serotonin Receptors 5-HT6 and 5-HT7
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jcc.21643openalex-snapshot
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Knowledge-based scoring function to predict protein-ligand interactions
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An introduction to ROC analysis
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Functional, molecular and pharmacological advances in 5-HT receptor research
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Hierarchical virtual screening approaches in small molecule drug discovery
inferredcites →https://doi.org/10.1016/s0022-2836(95)80037-9openalex-snapshot
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
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Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci100263popenalex-snapshot
Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods
inferredcites →https://doi.org/10.1021/ci100369fopenalex-snapshot
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
inferredcites →https://doi.org/10.1021/ci300463gopenalex-snapshot
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking
inferredcites →https://doi.org/10.1021/ci500001fopenalex-snapshot
Impact of Template Choice on Homology Model Efficiency in Virtual Screening
inferredcites →https://doi.org/10.1021/jm0200299openalex-snapshot
Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm050826hopenalex-snapshot
Homology Modeling of the Serotonin 5-HT1AReceptor Using Automated Docking of Bioactive Compounds with Defined Geometry
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jp020547vopenalex-snapshot
The Electronegativity Equalization Method II: Applicability of Different Atomic Charge Schemes
inferredcites →https://doi.org/10.1023/a:1008781006867openalex-snapshot
Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1038/nature09746openalex-snapshot
The structural basis for agonist and partial agonist action on a β1-adrenergic receptor
inferredcites →https://doi.org/10.1038/nature10236openalex-snapshot
Structure of the human histamine H1 receptor complex with doxepin
inferredcites →https://doi.org/10.1038/nature10753openalex-snapshot
Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist
inferredcites →https://doi.org/10.1038/nature10867openalex-snapshot
Structure and dynamics of the M3 muscarinic acetylcholine receptor
inferredcites →https://doi.org/10.1038/sj.npp.1301503openalex-snapshot
Neuropharmacological Profile of Novel and Selective 5-HT6 Receptor Agonists: WAY-181187 and WAY-208466
inferredcites →https://doi.org/10.1039/b409813gopenalex-snapshot
Molecular similarity: a key technique in molecular informatics
inferredcites →https://doi.org/10.1093/database/bar009openalex-snapshot
UniProt Knowledgebase: a hub of integrated protein data
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1126/science.1150577openalex-snapshot
High-Resolution Crystal Structure of an Engineered Human β 2 -Adrenergic G Protein–Coupled Receptor
inferredcites →https://doi.org/10.1126/science.1194396openalex-snapshot
Structures of the CXCR4 Chemokine GPCR with Small-Molecule and Cyclic Peptide Antagonists
inferredcites →https://doi.org/10.1126/science.1197410openalex-snapshot
Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist
inferredcites →https://doi.org/10.1126/science.1202793openalex-snapshot
Structure of an Agonist-Bound Human A 2A Adenosine Receptor
inferredcites →https://doi.org/10.1126/science.1232807openalex-snapshot
Structural Basis for Molecular Recognition at Serotonin Receptors
inferredcites →https://doi.org/10.1126/science.1232808openalex-snapshot
Structural Features for Functional Selectivity at Serotonin Receptors
inferredcites →https://doi.org/10.1145/1656274.1656278openalex-snapshot
The WEKA data mining software
inferredcites →https://doi.org/10.1186/1471-2164-13-s4-s2openalex-snapshot
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_15openalex-snapshot
Computational Modeling of Drugs for Alzheimer’s Disease: Design of Serotonin 5-HT6 Antagonists
inferred← citeshttps://doi.org/10.1007/s10822-015-9883-yopenalex-snapshot
Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor
inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00004-7openalex-snapshot
Post-processing of Docking Results: Tools and Strategies
inferred← citeshttps://doi.org/10.1016/j.coph.2016.07.007openalex-snapshot
Molecular interaction fingerprint approaches for GPCR drug discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00589openalex-snapshot
Pharmacoprint: A Combination of a Pharmacophore Fingerprint and Artificial Intelligence as a Tool for Computer-Aided Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00046openalex-snapshot
TIDAL: Topology-Inferred Drug Addiction Learning
inferred← citeshttps://doi.org/10.1080/17460441.2021.1929921openalex-snapshot
Computational representations of protein–ligand interfaces for structure-based virtual screening
inferred← citeshttps://doi.org/10.1109/tvt.2019.2893675openalex-snapshot
LSTM-based SQL Injection Detection Method for Intelligent Transportation System
inferred← citeshttps://doi.org/10.1186/s13321-018-0302-yopenalex-snapshot
Life beyond the Tanimoto coefficient: similarity measures for interaction fingerprints
inferred← citeshttps://doi.org/10.1371/journal.pone.0146666openalex-snapshot
Average Information Content Maximization—A New Approach for Fingerprint Hybridization and Reduction
inferred← citeshttps://doi.org/10.3389/fchem.2018.00138openalex-snapshot
Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds
inferred← citeshttps://doi.org/10.3390/biom10020349openalex-snapshot
N-(2-Hydroxyphenyl)-1-[3-(2-oxo-2,3-dihydro-1H- benzimidazol-1-yl)propyl]piperidine-4-Carboxamide (D2AAK4), a Multi-Target Ligand of Aminergic GPCRs, as a Potential Antipsychotic
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