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

Related outputs

Microbial Proteomics
Patel, H. and Whitehouse, D. 2019. Microbial Proteomics. in: Rapley, R. and Whitehouse, D. (ed.) Genomics and Clinical Diagnostics The Royal Society of Chemistry. pp. 103-139

Prediction of ligands to universally conserved binding sites of the influenza A virus nuclear export protein
Patel, H. and Kukol, A 2019. Prediction of ligands to universally conserved binding sites of the influenza A virus nuclear export protein. Virology. 537, pp. 97-103. https://doi.org/10.1016/j.virol.2019.08.013

Evolutionary conservation of influenza A PB2 sequences reveals potential target sites for small molecule inhibitors.
Patel, H. and Kukol, A 2017. Evolutionary conservation of influenza A PB2 sequences reveals potential target sites for small molecule inhibitors. Virology. 509, pp. 112-120. https://doi.org/10.1016/j.virol.2017.06.009

Recent discoveries of influenza A drug target sites to combat virus replication
Patel, H. and Kukol, A 2016. Recent discoveries of influenza A drug target sites to combat virus replication. Biochemical Society Transactions. 44 (3), pp. 932-936. https://doi.org/10.1042/BST20160002

Influenza A nucleoprotein binding sites for antivirals: current research and future potential
Patel, H. and Kukol, A 2014. Influenza A nucleoprotein binding sites for antivirals: current research and future potential. Future Virology. 9, pp. 625-627. https://doi.org/10.2217/fvl.14.45

Permalink - https://westminsterresearch.westminster.ac.uk/item/qz618/evaluation-of-a-novel-virtual-screening-strategy-using-receptor-decoy-binding-sites


Share this
Tweet
Email

Usage statistics

2 total views
5 total downloads
0 views this month
1 downloads this month
These values are for the period from September 2nd 2018, when this repository was created

Export as