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Better than Random? The Chemotype Enrichment Problem
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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/prot.20088openalex-snapshot
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot
Comparing protein–ligand docking programs is difficult
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
inferredcites →https://doi.org/10.1007/s10822-007-9151-xopenalex-snapshot
Bias, reporting, and sharing: computational evaluations of docking methods
inferredcites →https://doi.org/10.1007/s10822-007-9166-3openalex-snapshot
How to do an evaluation: pitfalls and traps
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/s10822-008-9170-2openalex-snapshot
What do we know and when do we know it?
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
inferredcites →https://doi.org/10.1007/s10822-008-9196-5openalex-snapshot
Recommendations for evaluation of computational methods
inferredcites →https://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferredcites →https://doi.org/10.1016/j.patrec.2005.10.010openalex-snapshot
An introduction to ROC analysis
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/ci020055fopenalex-snapshot
Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening
inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot
Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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/ci0503255openalex-snapshot
On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
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/ci700130jopenalex-snapshot
A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS
inferredcites →https://doi.org/10.1021/ci700415gopenalex-snapshot
Comparison of Ligand-Based and Receptor-Based Virtual Screening of HIV Entry Inhibitors for the CXCR4 and CCR5 Receptors Using 3D Ligand Shape Matching and Ligand−Receptor Docking
inferredcites →https://doi.org/10.1021/ci950274jopenalex-snapshot
Chemical Similarity Using Physiochemical Property Descriptors
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/jm049798dopenalex-snapshot
Comparison of Automated Docking Programs as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm0582165openalex-snapshot
Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm060763iopenalex-snapshot
Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein−Ligand Binding
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot
The Properties of Known Drugs. 1. Molecular Frameworks
inferredcites →https://doi.org/10.1201/9781420028775openalex-snapshot
Virtual Screening in Drug Discovery
inferredcites →https://doi.org/10.2174/092986706778521797openalex-snapshot
Docking and Scoring - Theoretically Easy, Practically Impossible?
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Chemoinformatic Characterization of the Chemical Space and Molecular Diversity of Compound Libraries
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Challenges and advances in computational docking: 2009 in review
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Using Spherical Harmonic Surface Property Representations for Ligand‐Based Virtual Screening
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Scaffold Diversity Analysis of Compound Data Sets Using an Entropy‐Based Measure
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Toward generalizable structure‐based deep learning models for protein–ligand interaction prediction: Challenges and strategies
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(How to) Profit from Molecular Dynamics-based Ensemble Docking
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2/3D Pharmacophore Definitions and Their Application
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Lessons and Successes in the Use of Molecular Fields
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Best Practices for Docking-Based Virtual Screening
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2/3D Pharmacophore definitions and their application
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Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-β-d-glucopyranosylamines
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Optimization of 5-arylidene barbiturates as potent, selective, reversible LSD1 inhibitors for the treatment of acute promyelocytic leukemia
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Discovery and optimization of novel small-molecule HIV-1 entry inhibitors using field-based virtual screening and bioisosteric replacement
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Core chemotype diversification in the HIV-1 entry inhibitor class using field-based bioisosteric replacement
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‘Fuzziness’ in pharmacophore-based virtual screening and de novo design
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Impact of the CXCR4 structure on docking-based virtual screening of HIV entry inhibitors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.01.003openalex-snapshot
Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00545openalex-snapshot
Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein–Protein Interfaces
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00850openalex-snapshot
Topological Similarity Search in Large Combinatorial Fragment Spaces
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00134openalex-snapshot
VS-APPLE: A Virtual Screening Algorithm Using Promiscuous Protein–Ligand Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00475openalex-snapshot
pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00660openalex-snapshot
GPCR-Bench: A Benchmarking Set and Practitioners’ Guide for G Protein-Coupled Receptor Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00571openalex-snapshot
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration
inferred← citeshttps://doi.org/10.1021/ci100073wopenalex-snapshot
Large-Scale Learning of Structure−Activity Relationships Using a Linear Support Vector Machine and Problem-Specific Metrics
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Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods
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Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing
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Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening
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PLS-DA - Docking Optimized Combined Energetic Terms (PLSDA-DOCET) Protocol: A Brief Evaluation
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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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Potential and Limitations of Ensemble Docking
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Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations
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Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance
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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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SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites
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An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors
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Maximum Common Substructure-Based Data Fusion in Similarity Searching
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Critical Comparison of Virtual Screening Methods against the MUV Data Set
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Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation
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Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
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Three-Dimensional Pharmacophore Methods in Drug Discovery
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Discriminating multiple motor imageries of human hands using EEG
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Optimization and visualization of the edge weights in optimal assignment methods for virtual screening
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Optimal assignment methods for ligand-based virtual screening
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Application of 3D Zernike descriptors to shape-based ligand similarity searching
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4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening
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Open-source platform to benchmark fingerprints for ligand-based virtual screening
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Efficient and biologically relevant consensus strategy for Parkinson’s disease gene prioritization
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Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis
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Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors
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Combined Pharmacophore Modeling, 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Indolyl-aryl-sulfone Derivatives as New HIV1 Inhibitors
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Importance of consensus region of multiple-ligand templates in a virtual screening method
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Combining Virtual Screening Protocol and In Vitro Evaluation towards the Discovery of BACE1 Inhibitors
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Virtual Screening–Guided Identification of Candidate USP7-Inhibitory Scaffolds Exhibiting Antiproliferative Activity
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Modeling Approaches for Ligand-Based 3D Similarity
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Challenges and Advances in Structure-Based Virtual Screening
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