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An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

https://doi.org/10.1021/ci500062f
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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QSAR Modeling of GPCR Ligands: Methodologies and Examples of Applications
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Pharmacophore-Based Virtual Screening
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Similarity Searching Using 2D Structural Fingerprints
inferredcites →https://doi.org/10.1007/s10822-007-9167-2openalex-snapshot
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
inferredcites →https://doi.org/10.1007/s10822-008-9181-zopenalex-snapshot
Managing bias in ROC curves
inferredcites →https://doi.org/10.1007/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
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Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands
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Lead Finder docking and virtual screening evaluation with Astex and DUD test sets
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Exploring structure–selectivity relationships of biogenic amine GPCR antagonists using similarity searching and dynamic compound mapping
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From purified GPCRs to drug discovery: the promise of protein-based methodologies
inferredcites →https://doi.org/10.1016/j.drudis.2006.10.005openalex-snapshot
Similarity-based virtual screening using 2D fingerprints
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Pharmacophore modeling and applications in drug discovery: challenges and recent advances
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Identification of structural determinants of ligand selectivity in 5-HT2 receptor subtypes on the basis of protein–ligand interactions
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An introduction to ROC analysis
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New insights from structural biology into the druggability of G protein-coupled receptors
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Purification of the beta-adrenergic receptor. Identification of the hormone binding subunit.
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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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PZIM: A Method for Similarity Searching Using Atom Environments and 2D Alignment
inferredcites →https://doi.org/10.1021/ci100374fopenalex-snapshot
Virtual Decoy Sets for Molecular Docking Benchmarks
inferredcites →https://doi.org/10.1021/ci200043zopenalex-snapshot
G-Protein Coupled Receptors Virtual Screening Using Genetic Algorithm Focused Chemical Space
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DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/ci200309jopenalex-snapshot
REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications
inferredcites →https://doi.org/10.1021/ci200412popenalex-snapshot
Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors
inferredcites →https://doi.org/10.1021/ci2005274openalex-snapshot
Comparative Analysis of Pharmacophore Screening Tools
inferredcites →https://doi.org/10.1021/ci200528dopenalex-snapshot
Recognizing Pitfalls in Virtual Screening: A Critical Review
inferredcites →https://doi.org/10.1021/ci300030uopenalex-snapshot
Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci3001277openalex-snapshot
ZINC: A Free Tool to Discover Chemistry for Biology
inferredcites →https://doi.org/10.1021/ci300510nopenalex-snapshot
FINDSITE comb : A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach
inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci700099uopenalex-snapshot
Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics
inferredcites →https://doi.org/10.1021/ci700404copenalex-snapshot
Combinatorial QSAR Modeling of Specificity and Subtype Selectivity of Ligands Binding to Serotonin Receptors 5HT1E and 5HT1F
inferredcites →https://doi.org/10.1021/ci8002649openalex-snapshot
Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
inferredcites →https://doi.org/10.1021/ci800303kopenalex-snapshot
Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm200371qopenalex-snapshot
Progress in Structure Based Drug Design for G Protein-Coupled Receptors
inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot
The Properties of Known Drugs. 1. Molecular Frameworks
inferredcites →https://doi.org/10.1038/aps.2011.187openalex-snapshot
Ice breaking in GPCR structural biology
inferredcites →https://doi.org/10.1038/nature08506openalex-snapshot
Predicting new molecular targets for known drugs
inferredcites →https://doi.org/10.1038/nchembio.1025openalex-snapshot
A new era of GPCR structural and chemical biology
inferredcites →https://doi.org/10.1038/nrd2199openalex-snapshot
How many drug targets are there?
inferredcites →https://doi.org/10.1038/nrd3320openalex-snapshot
G protein-coupled receptors: novel targets for drug discovery in cancer
inferredcites →https://doi.org/10.1038/nrd3859openalex-snapshot
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function
inferredcites →https://doi.org/10.1093/bioinformatics/bts249openalex-snapshot
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
inferredcites →https://doi.org/10.1093/nar/gkm948openalex-snapshot
GLIDA: GPCR ligand database for chemical genomics drug discovery database and tools update
inferredcites →https://doi.org/10.1093/nar/gkp456openalex-snapshot
PubChem: a public information system for analyzing bioactivities of small molecules
inferredcites →https://doi.org/10.1111/j.1747-0285.2009.00944.xopenalex-snapshot
Using Ligand‐Based Virtual Screening to Allosterically Stabilize the Activated State of a GPCR
inferredcites →https://doi.org/10.1186/1758-2946-1-14openalex-snapshot
Optimal assignment methods for ligand-based virtual screening
inferredcites →https://doi.org/10.18388/abp.2012_2086openalex-snapshot
G protein-coupled receptors--recent advances.
inferredcites →https://doi.org/10.2174/092986708784049630openalex-snapshot
Pharmacophore-Based Virtual Screening
inferredcites →https://doi.org/10.2174/092986711795933669openalex-snapshot
Pharmacophore Modelling: A Forty Year Old Approach and its Modern Synergies
inferredcites →https://doi.org/10.2174/1381612053507549openalex-snapshot
New Methodologies for Ligand-Based Virtual Screening
inferredcites →https://doi.org/10.2174/138161207782794257openalex-snapshot
Predictive QSAR Modeling Workflow, Model Applicability Domains, and Virtual Screening
inferredcites →https://doi.org/10.2174/138620711797537120openalex-snapshot
Current Trends in Virtual High Throughput Screening Using Ligand-Based and Structure-Based Methods
inferredcites →https://doi.org/10.2174/157340910790980151openalex-snapshot
Pharmacophore Based Drug Design Approach as a Practical Process in Drug Discovery
inferredcites →https://doi.org/10.3390/molecules18010735openalex-snapshot
Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

What points at this work

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MUBD‐DecoyMaker 2.0: A Python GUI Application to Generate Maximal Unbiased Benchmarking Data Sets for Virtual Drug Screening
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HDAC3i‐Finder: A Machine Learning‐based Computational Tool to Screen for HDAC3 Inhibitors
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Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis
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Evaluation of Cross-Validation Strategies in Sequence-Based Binding Prediction Using Deep Learning
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Additional file 1 of Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison
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