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Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
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Community benchmarks for virtual screening
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Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
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Highly selective c-Jun N-terminal kinase (JNK) 2 and 3 inhibitors with in vitro CNS-like pharmacokinetic properties prevent neurodegeneration
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MMP-13 selective α-sulfone hydroxamates: A survey of P1′ heterocyclic amide isosteres
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Synthesis and structure-activity relationship of 4-(1,3-benzothiazol-2-yl)-thiophene-2-sulfonamides as cyclin-dependent kinase 5 (cdk5)/p25 inhibitors
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Combination of ligand- and structure-based methods in virtual screening
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Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods
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The protein data bank: A computer-based archival file for macromolecular structures
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Selective Inactivation of a Human Neuronal Silencing Phosphatase by a Small Molecule Inhibitor
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Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier
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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance
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A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
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Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
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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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Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods
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Locating Sweet Spots for Screening Hits and Evaluating Pan-Assay Interference Filters from the Performance Analysis of Two Lead-like Libraries
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Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking
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An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors
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Kernel Density Estimation Applied to Bond Length, Bond Angle, and Torsion Angle Distributions
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Comparison of Topological, Shape, and Docking Methods in Virtual Screening
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FieldScreen: Virtual Screening Using Molecular Fields. Application to the DUD Data Set
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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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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K a Predictions
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Additivity methods in molecular polarizability
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
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Comparison of Shape-Matching and Docking as Virtual Screening Tools
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Benchmarking Sets for Molecular Docking
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Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery
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Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
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Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening
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Structure-Based Optimization of Arylamides as Inhibitors of Soluble Epoxide Hydrolase
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Multidentate Small-Molecule Inhibitors of Vaccinia H1-Related (VHR) Phosphatase Decrease Proliferation of Cervix Cancer Cells
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New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
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The Properties of Known Drugs. 1. Molecular Frameworks
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Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
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Structural enrichment of HTS compounds from available commercial libraries
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Virtual screening of bioassay data
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Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Quantum Computing and Its Promise in Drug Discovery
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Peripheral Inhibition of Small C‐Terminal Domain Phosphatase 1 With Napthoquinone Analogs
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Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction
inferred← citeshttps://doi.org/10.1002/minf.201700120openalex-snapshot
Prediction of Protein−compound Binding Energies from Known Activity Data: Docking‐score‐based Method and its Applications
inferred← citeshttps://doi.org/10.1002/minf.202200103openalex-snapshot
Critical Assessment of State‐of‐the‐Art Ligand‐Based Virtual Screening Methods
inferred← citeshttps://doi.org/10.1007/s10822-018-0155-5openalex-snapshot
Rescoring of docking poses under Occam’s Razor: are there simpler solutions?
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Binary classification of imbalanced datasets using conformal prediction
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Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives
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Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models
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AI Accelerated Chemical Screening Integrates ChemBERTa to Identify Repositionable CASP4 Inhibitors via MD Simulations and MM/PBSA Analysis
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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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In Silico Exploration for Novel Type-I Inhibitors of Tie-2/TEK: The Performance of Different Selection Strategy in Selecting Virtual Screening Candidates
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Contrôle qualité des chimiothèques
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PASS Targets: Ligand-based multi-target computational system based on a public data and naïve Bayes approach
inferred← citeshttps://doi.org/10.1080/17460441.2016.1216967openalex-snapshot
Getting the most out of PubChem for virtual screening
inferred← citeshttps://doi.org/10.1093/bib/bbab135openalex-snapshot
Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors
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Phomoarcherin B as a novel HIV-1 reverse transcriptase RNase H activity inhibitor: conclusions from comprehensive computational analysis
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Enrichment Assessment of Multiple Virtual Screening Strategies for Toll‐Like Receptor 8 Agonists Based on a Maximal Unbiased Benchmarking Data Set
inferred← citeshttps://doi.org/10.1186/s12859-017-1845-zopenalex-snapshot
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization
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Efficient iterative virtual screening with Apache Spark and conformal prediction
inferred← citeshttps://doi.org/10.3389/fphar.2018.00983openalex-snapshot
Discovery of Potent Disheveled/Dvl Inhibitors Using Virtual Screening Optimized With NMR-Based Docking Performance Index
inferred← citeshttps://doi.org/10.3390/ijms21124380openalex-snapshot
Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement
inferred← citeshttps://doi.org/10.3390/life10050057openalex-snapshot
Targeting the C-Terminal Domain Small Phosphatase 1
inferred← citeshttps://doi.org/10.70675/c9cacc57zdf38z489bzacf8z0d5ecf73c80copenalex-snapshot
Development of new virtual screening methods and novel unbiased benchmarking data sets
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