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
| Title | Evaluation of a novel virtual screening strategy using receptor decoy binding sites |
|---|---|
| Type | Journal article |
| Authors | Patel, 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. |
| Keywords | Virtual screening, docking, receptor, decoy, Autodock |
| Journal | Journal of Negative Results in BioMedicine |
| Journal citation | 15, pp. 1-5 |
| ISSN | 1477-5751 |
| Year | 2016 |
| Publisher | BioMed 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 ID | 27553084 |
| Web address (URL) | https://jnrbm.biomedcentral.com/articles/10.1186/s12952-016-0058-8 |
| Publication dates | |
| Published | 23 Aug 2016 |
| Funder | University of Hertfordshire |