Title |
Evaluation of a novel virtual screening strategy using receptor decoy binding sites
|
---|---|
Published in |
Journal of Negative Results in BioMedicine, August 2016
|
DOI | 10.1186/s12952-016-0058-8 |
Pubmed ID | |
Authors |
Hershna Patel, Andreas Kukol |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Japan | 1 | 100% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 22 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 5 | 23% |
Student > Bachelor | 3 | 14% |
Researcher | 2 | 9% |
Student > Postgraduate | 2 | 9% |
Student > Master | 2 | 9% |
Other | 3 | 14% |
Unknown | 5 | 23% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 4 | 18% |
Chemistry | 3 | 14% |
Agricultural and Biological Sciences | 2 | 9% |
Mathematics | 1 | 5% |
Nursing and Health Professions | 1 | 5% |
Other | 5 | 23% |
Unknown | 6 | 27% |