Evaluation of a novel virtual screening strategy using receptor decoy binding sites

Patel, H. and Kukol, A. 2016. Evaluation of a novel virtual screening strategy using receptor decoy binding sites. Journal of Negative Results in BioMedicine. 15, pp. 1-5. https://doi.org/10.1186/s12952-016-0058-8

TitleEvaluation of a novel virtual screening strategy using receptor decoy binding sites
TypeJournal article
AuthorsPatel, H.
Kukol, A.
Abstract

Virtual screening is used in biomedical research to predict the binding affinity of a large set of small organic molecules to protein receptor targets. This report shows the development and evaluation of a novel yet straightforward attempt to improve this ranking in receptor-based molecular docking using a receptor-decoy strategy. This strategy includes defining a decoy binding site on the receptor and adjusting the ranking of the true binding-site virtual screen based on the decoy-site screen. The results show that by docking against a receptor-decoy site with Autodock Vina, improved Receiver Operator Characteristic Enrichment (ROCE) was achieved for 5 out of fifteen receptor targets investigated, when up to 15 % of a decoy site rank list was considered. No improved enrichment was seen for 7 targets, while for 3 targets the ROCE was reduced. The extent to which this strategy can effectively improve ligand prediction is dependent on the target receptor investigated.

KeywordsVirtual screening, docking, receptor, decoy, Autodock
JournalJournal of Negative Results in BioMedicine
Journal citation15, pp. 1-5
ISSN1477-5751
Year2016
PublisherBioMed Central
Publisher's version
License
CC BY 4.0
File Access Level
Open (open metadata and files)
Digital Object Identifier (DOI)https://doi.org/10.1186/s12952-016-0058-8
PubMed ID27553084
Web address (URL)https://jnrbm.biomedcentral.com/articles/10.1186/s12952-016-0058-8
Publication dates
Published23 Aug 2016

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