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REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications

https://doi.org/10.1021/ci200309j

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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/cmdc.200700151openalex-snapshot

Virtual Screening for Selective Allosteric mGluR1 Antagonists and Structure–Activity Relationship Investigations for Coumarine Derivatives

inferredcites →https://doi.org/10.1002/qsar.200610091openalex-snapshot

Scaffold‐Hopping: How Far Can You Jump?

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/s10822-007-9167-2openalex-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/s10822-008-9196-5openalex-snapshot

Recommendations for evaluation of computational methods

inferredcites →https://doi.org/10.1016/j.bmc.2006.10.013openalex-snapshot

3D pharmacophore based virtual screening of T-type calcium channel blockers

inferredcites →https://doi.org/10.1016/j.bmc.2007.03.019openalex-snapshot

First pharmacophore-based identification of androgen receptor down-regulating agents: Discovery of potent anti-prostate cancer agents

inferredcites →https://doi.org/10.1016/j.bmcl.2006.06.057openalex-snapshot

Pharmacophore-based virtual screening: The discovery of novel methionyl-tRNA synthetase inhibitors

inferredcites →https://doi.org/10.1016/j.bmcl.2010.06.103openalex-snapshot

Discovery of novel α7 nicotinic receptor antagonists

inferredcites →https://doi.org/10.1016/j.bmcl.2010.07.043openalex-snapshot

Identification of a novel NR2B-selective NMDA receptor antagonist using a virtual screening approach

inferredcites →https://doi.org/10.1016/j.bmcl.2010.10.051openalex-snapshot

Discovery of a novel IKK-β inhibitor by ligand-based virtual screening techniques

inferredcites →https://doi.org/10.1016/j.drudis.2011.02.011openalex-snapshot

State-of-the-art in ligand-based virtual screening

inferredcites →https://doi.org/10.1016/j.ejmech.2009.05.003openalex-snapshot

An efficient steroid pharmacophore-based strategy to identify new aromatase inhibitors

inferredcites →https://doi.org/10.1016/j.ejmech.2010.06.034openalex-snapshot

Discovery of novel CDK1 inhibitors by combining pharmacophore modeling, QSAR analysis and in silico screening followed by in vitro bioassay

inferredcites →https://doi.org/10.1016/j.ejmech.2011.03.040openalex-snapshot

Discovery of new nanomolar peroxisome proliferator-activated receptor γ activators via elaborate ligand-based modeling

inferredcites →https://doi.org/10.1016/s0960-894x(02)00943-5openalex-snapshot

Pharmacophore-Based discovery of substituted pyridines as novel dopamine transporter inhibitors

inferredcites →https://doi.org/10.1021/ci00021a032openalex-snapshot

National Cancer Institute Drug Information System 3D Database

inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

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/ci100222kopenalex-snapshot

Elaborate Ligand-Based Modeling Reveals New Nanomolar Heat Shock Protein 90α Inhibitors

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/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/ci900419kopenalex-snapshot

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

inferredcites →https://doi.org/10.1021/jm010433sopenalex-snapshot

Novel Lead Generation through Hypothetical Pharmacophore Three-Dimensional Database Searching: Discovery of Isoflavonoids as Nonsteroidal Inhibitors of Rat 5α-Reductase

inferredcites →https://doi.org/10.1021/jm031041jopenalex-snapshot

Chemical Function Based Pharmacophore Generation of Endothelin-A Selective Receptor Antagonists

inferredcites →https://doi.org/10.1021/jm0604373openalex-snapshot

Calcium Channel Antagonists Discovered by a Multidisciplinary Approach

inferredcites →https://doi.org/10.1021/jm060655wopenalex-snapshot

Identification of Natural-Product-Derived Inhibitors of 5-Lipoxygenase Activity by Ligand-Based Virtual Screening

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

inferredcites →https://doi.org/10.1021/jm100492zopenalex-snapshot

Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening

inferredcites →https://doi.org/10.1021/jm1010012openalex-snapshot

Virtual Screening to Identify Novel Antagonists for the G Protein-Coupled NK3Receptor

inferredcites →https://doi.org/10.1021/jm101020zopenalex-snapshot

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

inferredcites →https://doi.org/10.1021/jm101080vopenalex-snapshot

Discovery of Non-Glycoside Sodium-Dependent Glucose Co-Transporter 2 (SGLT2) Inhibitors by Ligand-Based Virtual Screening

inferredcites →https://doi.org/10.1021/jm101309gopenalex-snapshot

Pharmacophore Modeling and Virtual Screening for Novel Acidic Inhibitors of Microsomal Prostaglandin E2 Synthase-1 (mPGES-1)

inferredcites →https://doi.org/10.1021/jm200139jopenalex-snapshot

SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 2. Prospective Case Study in the Discovery of Diverse p90 Ribosomal S6 Protein Kinase 2 Inhibitors To Suppress Cell Migration

inferredcites →https://doi.org/10.1021/jm800151nopenalex-snapshot

Discovery of Novel and Cardioselective Diltiazem-like Calcium Channel Blockers via Virtual Screening

inferredcites →https://doi.org/10.1021/jm801278gopenalex-snapshot

Discovery of Novel Myc−Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model

inferredcites →https://doi.org/10.1021/jm901718zopenalex-snapshot

Pharmacophore Development and Application Toward the Identification of Novel, Small-Molecule Autotaxin Inhibitors

inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot

The Properties of Known Drugs. 1. Molecular Frameworks

inferredcites →https://doi.org/10.1038/nchembio.150openalex-snapshot

Identification of a chemical probe for NAADP by virtual screening

inferredcites →https://doi.org/10.1093/nar/gkm958openalex-snapshot

DrugBank: a knowledgebase for drugs, drug actions and drug targets

inferredcites →https://doi.org/10.1111/j.1747-0285.2011.01089.xopenalex-snapshot

New Uses for Old Drugs: Pharmacophore‐Based Screening for the Discovery of P‐Glycoprotein Inhibitors

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118618110.ch15openalex-snapshot

Virtual Screening Methods

inferred← citeshttps://doi.org/10.1002/9781118742785.ch6openalex-snapshot

CRITICAL ASSESSMENT OF VIRTUAL SCREENING FOR HIT IDENTIFICATION

inferred← citeshttps://doi.org/10.1002/wcms.1106openalex-snapshot

Computational methods for scaffold hopping

inferred← citeshttps://doi.org/10.1002/wcms.1128openalex-snapshot

Shape‐based similarity searching in chemical databases

inferred← citeshttps://doi.org/10.1016/j.sbi.2018.01.006openalex-snapshot

Statistical and machine learning approaches to predicting protein–ligand interactions

inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.11.015openalex-snapshot

Benchmarking methods and data sets for ligand enrichment assessment in virtual screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00090openalex-snapshot

Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00403openalex-snapshot

Most Ligand-Based Classification Benchmarks Reward Memorization Rather than Generalization

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00004openalex-snapshot

Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00689openalex-snapshot

Development of New Methods Needs Proper Evaluation—Benchmarking Sets for Machine Learning Experiments for Class A GPCRs

inferred← citeshttps://doi.org/10.1021/bk-2019-1326.ch005openalex-snapshot

Using Machine Learning To Inform Decisions in Drug Discovery: An Industry Perspective

inferred← citeshttps://doi.org/10.1021/ci500062fopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/jm300687eopenalex-snapshot

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

inferred← citeshttps://doi.org/10.1111/cbdd.12590openalex-snapshot

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/10.1146/annurev-biodatasci-122120-124216openalex-snapshot

Machine Learning in Chemoinformatics and Medicinal Chemistry

inferred← citeshttps://doi.org/10.1186/s12859-018-2248-5openalex-snapshot

SimCAL: a flexible tool to compute biochemical reaction similarity

inferred← citeshttps://doi.org/10.12688/f1000research.1-11.v1openalex-snapshot

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications

inferred← citeshttps://doi.org/10.12688/f1000research.3713.1openalex-snapshot

Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer

inferred← citeshttps://doi.org/10.3389/fchem.2021.662688openalex-snapshot

Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products

inferred← citeshttps://doi.org/10.3389/fcimb.2022.838259openalex-snapshot

Biological Membrane-Penetrating Peptides: Computational Prediction and Applications

inferred← citeshttps://doi.org/10.3410/f1000research.1-11.v1openalex-snapshot

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications

inferred← citeshttps://doi.org/10.4155/fmc.12.19openalex-snapshot

Virtual Compound Screening In Drug Discovery

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