NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches
Joint Authors
Source
Computational and Mathematical Methods in Medicine
Issue
Vol. 2017, Issue 2017 (31 Dec. 2017), pp.1-16, 16 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2017-07-25
Country of Publication
Egypt
No. of Pages
16
Main Subjects
Abstract EN
Nucleotides play a central role in life-form metabolism, by interacting with proteins and mediating the function of proteins.
It is estimated that nucleotides constitute about 15% of the biologically relevant ligands included in PDB.
Prediction of binding sites of nucleotides is useful in understanding the function of proteins and can facilitate the in silico design of drugs.
In this study, we propose a nucleotide-binding site predictor, namely, NSiteMatch.
The NSiteMatch algorithm integrates three different strategies: geometrical analysis, energy calculation, and template comparison.
Unlike a traditional template-based predictor, which identifies global similarity between target structure and template, NSiteMatch concerns the local similarity between a surface patch of the target protein and the binding sites of template.
To this end, NSiteMatch identifies more templates than traditional template-based predictors.
The NSiteMatch predictor is compared with three representative methods, Findsite, Q-SiteFinder, and MetaPocket.
An extensive evaluation demonstrates that NSiteMatch achieves higher success rates than Findsite, Q-SiteFinder, and MetaPocket, in prediction of binding sites of ATP, ADP, and AMP.
American Psychological Association (APA)
Sun, Jie& Chen, Ke. 2017. NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches. Computational and Mathematical Methods in Medicine،Vol. 2017, no. 2017, pp.1-16.
https://search.emarefa.net/detail/BIM-1142196
Modern Language Association (MLA)
Sun, Jie& Chen, Ke. NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches. Computational and Mathematical Methods in Medicine No. 2017 (2017), pp.1-16.
https://search.emarefa.net/detail/BIM-1142196
American Medical Association (AMA)
Sun, Jie& Chen, Ke. NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches. Computational and Mathematical Methods in Medicine. 2017. Vol. 2017, no. 2017, pp.1-16.
https://search.emarefa.net/detail/BIM-1142196
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1142196