Open-source platform to benchmark fingerprints for ligand-based virtual screening

Inflation of correlation in the pursuit of drug-likeness

(2013) Peter W. Kenny et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets

(2012) Roberto Todeschini et al.   Journal of Chemical Information and Modeling

Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening

(2012) Guoping Hu et al.   Journal of Chemical Information and Modeling

Effectiveness of 2D fingerprints for scaffold hopping

(2011) Eleanor J Gardiner et al.   Future Medicinal Chemistry

Large-Scale Similarity Search Profiling of ChEMBL Compound Data Sets

(2011) Kathrin Heikamp et al.   Journal of Chemical Information and Modeling

How similar are those molecules after all? Use two descriptors and you will have three different answers

(2010) Andreas Bender   Expert Opinion on Drug Discovery

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

(2010) Vishwesh Venkatraman et al.   Journal of Chemical Information and Modeling

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

(2010) Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Extended-Connectivity Fingerprints

(2010) David Rogers et al.   Journal of Chemical Information and Modeling

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

(2010) Martin Vogt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set

(2009) Modest von Korff et al.   Journal of Chemical Information and Modeling

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

(2009) Andreas Bender et al.   Journal of Chemical Information and Modeling

Better than Random? The Chemotype Enrichment Problem

(2009) Mark D. Mackey et al.   Journal of Chemical Information and Modeling

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

(2009) Sebastian G. Rohrer et al.   Journal of Chemical Information and Modeling

Critical Comparison of Virtual Screening Methods against the MUV Data Set

(2009) Pekka Tiikkainen et al.   Journal of Chemical Information and Modeling

Alternative Global Goodness Metrics and Sensitivity Analysis:  Heuristics to Check the Robustness of Conclusions from Studies Comparing Virtual Screening Methods

(2008) Robert P. Sheridan   Journal of Chemical Information and Modeling

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

(2008) Sebastian G. Rohrer et al.   Journal of Chemical Information and Modeling

What do we know and when do we know it?

(2008) Anthony Nicholls   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recommendations for evaluation of computational methods

(2008) Ajay N. Jain et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Community benchmarks for virtual screening

(2008) John J. Irwin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN