Title:
DBD-Hunter: a knowledge-based method for the prediction of DNA protein interactions
DBD-Hunter: a knowledge-based method for the prediction of DNA protein interactions
| dc.contributor.author | Gao, Mu | |
| dc.contributor.author | Skolnick, Jeffrey | |
| dc.contributor.corporatename | Georgia Institute of Technology. Center for the Study of Systems Biology | |
| dc.date.accessioned | 2009-01-28T15:06:35Z | |
| dc.date.available | 2009-01-28T15:06:35Z | |
| dc.date.issued | 2008-05-31 | |
| dc.description | © 2008 The Authors. Published byOxford University Press. The definitive version is available online at: http://nar.oxfordjournals.org/cgi/content/full/36/12/3978 | en |
| dc.description | doi:10.1093/nar/gkn332 | |
| dc.description.abstract | The structures of DNA–protein complexes have illuminated the diversity of DNA–protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA–protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In benchmark tests on ~4000 proteins, our method achieved an accuracy of 98% and a precision of 84%, which significantly outperforms three previous methods. We further validate the method on DNAbinding protein structures determined in DNA-free (apo) state. Weshow that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. Finally, we apply the method to ~1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. | en |
| dc.identifier.citation | Nucleic Acids Research 2008 36(12):3978-3992 | en |
| dc.identifier.issn | 0305-1048 | |
| dc.identifier.uri | http://hdl.handle.net/1853/26729 | |
| dc.language.iso | en_US | en |
| dc.publisher | Georgia Institute of Technology | en |
| dc.publisher.original | Oxford University Press | |
| dc.subject | Computational biology | en |
| dc.subject | Protein structure | en |
| dc.subject | DNA-binding proteins | en |
| dc.subject | Knowledge-based systems | en |
| dc.title | DBD-Hunter: a knowledge-based method for the prediction of DNA protein interactions | en |
| dc.type | Text | |
| dc.type.genre | Article | |
| dspace.entity.type | Publication | |
| local.contributor.author | Skolnick, Jeffrey | |
| local.contributor.corporatename | College of Sciences | |
| local.contributor.corporatename | School of Biological Sciences | |
| local.contributor.corporatename | Center for the Study of Systems Biology | |
| relation.isAuthorOfPublication | 80f29357-f18b-4635-abd1-628d627d301d | |
| relation.isOrgUnitOfPublication | 85042be6-2d68-4e07-b384-e1f908fae48a | |
| relation.isOrgUnitOfPublication | c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5 | |
| relation.isOrgUnitOfPublication | d3d635bd-b38e-4ef6-a2d0-0875b9a83e34 |