Protocol

Computational Drug Discovery and Design

Volume 819 of the series Methods in Molecular Biology pp 187-195

Date:

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

  • Andrew J. ChristoffersonAffiliated withNational Institute of Biological Sciences
  • , Niu HuangAffiliated withNational Institute of Biological Sciences Email author 

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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