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

Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Virtual screening Molecular docking Enrichment Decoys 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.National Institute of Biological SciencesBeijingPeople Republic of China

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