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Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics

https://doi.org/10.1021/ci700099u
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What this work says

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

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Drug Design Strategies for Targeting G-Protein-Coupled Receptors
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Virtual Screening for Bioactive Molecules
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Principal Component Analysis
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Self-Organizing Maps
inferredcites →https://doi.org/10.1007/s10822-004-4067-1openalex-snapshot
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
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D-optimal designs
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D-optimal onion designs in statistical molecular design
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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
inferredcites →https://doi.org/10.1016/s1088-467x(99)00013-xopenalex-snapshot
SOM-based data visualization methods
inferredcites →https://doi.org/10.1017/cbo9780511542039openalex-snapshot
Spatial Analysis
inferredcites →https://doi.org/10.1017/s0021900200094328openalex-snapshot
The second-order analysis of stationary point processes
inferredcites →https://doi.org/10.1021/ci0100144openalex-snapshot
Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches
inferredcites →https://doi.org/10.1021/ci034231bopenalex-snapshot
Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures
inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot
Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
inferredcites →https://doi.org/10.1021/ci0497861openalex-snapshot
Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease
inferredcites →https://doi.org/10.1021/ci049860fopenalex-snapshot
The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data
inferredcites →https://doi.org/10.1021/ci0498719openalex-snapshot
Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance
inferredcites →https://doi.org/10.1021/ci0500177openalex-snapshot
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
inferredcites →https://doi.org/10.1021/ci050034wopenalex-snapshot
Consensus Scoring Criteria for Improving Enrichment in Virtual Screening
inferredcites →https://doi.org/10.1021/ci050347ropenalex-snapshot
Scaffold Hopping Using Clique Detection Applied to Reduced Graphs
inferredcites →https://doi.org/10.1021/ci050372xopenalex-snapshot
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank
inferredcites →https://doi.org/10.1021/ci050457yopenalex-snapshot
ErG: 2D Pharmacophore Descriptions for Scaffold Hopping
inferredcites →https://doi.org/10.1021/ci050465eopenalex-snapshot
Training Similarity Measures for Specific Activities: Application to Reduced Graphs
inferredcites →https://doi.org/10.1021/ci050510iopenalex-snapshot
A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations
inferredcites →https://doi.org/10.1021/ci060013hopenalex-snapshot
R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method
inferredcites →https://doi.org/10.1021/ci6003493openalex-snapshot
Measuring CAMD Technique Performance. 2. How “Druglike” Are Drugs? Implications of Random Test Set Selection Exemplified Using Druglikeness Classification Models
inferredcites →https://doi.org/10.1021/ci600418uopenalex-snapshot
Introduction of an Information-Theoretic Method to Predict Recovery Rates of Active Compounds for Bayesian in Silico Screening: Theory and Screening Trials
inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot
Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
inferredcites →https://doi.org/10.1021/ci600541fopenalex-snapshot
Counting Clusters Using R-NN Curves
inferredcites →https://doi.org/10.1021/ci9501047openalex-snapshot
Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection
inferredcites →https://doi.org/10.1021/ci960373copenalex-snapshot
The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding
inferredcites →https://doi.org/10.1021/ci9800211openalex-snapshot
Chemical Similarity Searching
inferredcites →https://doi.org/10.1021/jm000375vopenalex-snapshot
Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm020155copenalex-snapshot
Do Structurally Similar Molecules Have Similar Biological Activity?
inferredcites →https://doi.org/10.1021/jm049092jopenalex-snapshot
Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4
inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot
Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data
inferredcites →https://doi.org/10.1021/jm051139topenalex-snapshot
Robust Ligand-Based Modeling of the Biological Targets of Known Drugs
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm960290nopenalex-snapshot
Neighborhood Behavior: A Useful Concept for Validation of “Molecular Diversity” Descriptors
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1039/b409865jopenalex-snapshot
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
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Some Guidelines for Constructing ExactD-Optimal Designs on Convex Design Spaces
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Spatial Data Analysis by Example
inferredcites →https://doi.org/10.1093/oso/9780198522546.001.0001openalex-snapshot
Optimum Experimental Designs
inferredcites →https://doi.org/10.1109/72.846731openalex-snapshot
Clustering of the self-organizing map
inferredcites →https://doi.org/10.2174/1381612053507549openalex-snapshot
New Methodologies for Ligand-Based Virtual Screening
inferredcites →https://doi.org/10.2307/1270278openalex-snapshot
Optimum Experimental Designs
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Spatial and Temporal Analysis in Ecology.

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cem.1240openalex-snapshot
The effect of structural redundancy in validation sets on virtual screening performance
inferred← citeshttps://doi.org/10.1007/978-1-61779-465-0_13openalex-snapshot
How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries
inferred← citeshttps://doi.org/10.1007/978-3-030-50420-5_44openalex-snapshot
Quantifying Overfitting Potential in Drug Binding Datasets
inferred← citeshttps://doi.org/10.1016/j.bbagen.2020.129545openalex-snapshot
Machine learning and ligand binding predictions: A review of data, methods, and obstacles
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Ligand-based Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies for Discovery of Potential Topoisomerase I Inhibitors
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Benchmarking methods and data sets for ligand enrichment assessment in virtual screening
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Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives
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Balancing Data Quantity and Quality: Evaluating Curation Strategies for Bioactivity Prediction in Lead Optimization
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DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
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REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications
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Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential
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Recognizing Pitfalls in Virtual Screening: A Critical Review
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Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets
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An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs
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Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT3A, Histamine H1, and Histamine H4Receptors
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How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space
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Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
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Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set
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Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors
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Shaping the interaction landscape of bioactive molecules
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Protein homology reveals new targets for bioactive small molecules
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MUVing SAFEly: Scale for Assessing Figures of Effectiveness (SAFE) in virtual screening using Maximum Unbiased Validation (MUV) datasets
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Inhibitors of Helicobacter pylori Protease HtrA Found by ‘Virtual Ligand’ Screening Combat Bacterial Invasion of Epithelia
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Développement d’outils statistiques d’évaluation de méthodes de criblage virtuel : courbes de prédictivité & Screening Explorer
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