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Computational Drug Discovery and Design pp 187–195Cite as

How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 819))

Abstract

Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.

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Acknowledgement

The Chinese Ministry of Science and Technology “863” Grant 2008AA022313 (to N.H.) is acknowledged for financial support and Shoichet Lab at UCSF for the DOCK3.5.54 program.

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Authors and Affiliations

  1. National Institute of Biological Sciences, Beijing, People Republic of China

    Andrew J. Christofferson & Niu Huang

Authors
  1. Andrew J. Christofferson
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  2. Niu Huang
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Corresponding author

Correspondence to Niu Huang .

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Editors and Affiliations

  1. University of Utah, 30 South 2000 East Rm 307, Salt Lake City, 84112-5820, California, USA

    Riccardo Baron

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Christofferson, A.J., Huang, N. (2012). How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries. In: Baron, R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 819. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-465-0_13

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  • DOI: https://doi.org/10.1007/978-1-61779-465-0_13

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-464-3

  • Online ISBN: 978-1-61779-465-0

  • eBook Packages: Springer Protocols

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