Full metadata record
DC FieldValueLanguage
dc.contributor.authorChen, Yung-Chiangen_US
dc.contributor.authorLo, Yu-Shuen_US
dc.contributor.authorHsu, Wen-Changen_US
dc.contributor.authorYang, Jinn-Moonen_US
dc.date.accessioned2014-12-08T15:13:44Z-
dc.date.available2014-12-08T15:13:44Z-
dc.date.issued2007-07-01en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://dx.doi.org/10.1093/nar/gkm346en_US
dc.identifier.urihttp://hdl.handle.net/11536/10619-
dc.description.abstractThe 3D-partner is a web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a new scoring function. 3D-partner first utilizes IMPALA to identify homologous structures (templates) of a query from a heterodimer profile library. The interacting-partner sequence profiles of these templates are then used to search interacting candidates of the query from protein sequence databases (e. g. SwissProt) by PSI-BLAST. We developed a new scoring function, which includes the contact-residue interacting score (e. g. the steric, hydrogen bonds, and electrostatic interactions) and the template consensus score (e. g. couple-conserved residue and the template similarity scores), to evaluate how well the interfaces between the query and interacting candidates. Based on this scoring function, 3D-partner provides the statistic significance, the binding models (e. g. hydrogen bonds and conserved amino acids) and functional annotations of interacting partners. The correlation between experimental energies and predicted binding affinities of our scoring function is 0.91 on 275 mutated residues from the ASEdb. The average precision of the server is 0.72 on 563 queries and the execution time of this server for a query is similar to 15s on average. These results suggest that the 3D-partner server can be useful in protein-protein interaction predictions and binding model visualizations. The server is available online at: http://3D-partner.life.nctu.edu.tw.en_US
dc.language.isoen_USen_US
dc.title3D-partner: a web server to infer interacting partners and binding modelsen_US
dc.typeArticleen_US
dc.identifier.doi10.1093/nar/gkm346en_US
dc.identifier.journalNUCLEIC ACIDS RESEARCHen_US
dc.citation.volume35en_US
dc.citation.issueen_US
dc.citation.spageW561en_US
dc.citation.epageW567en_US
dc.contributor.department生物科技學系zh_TW
dc.contributor.department生物資訊及系統生物研究所zh_TW
dc.contributor.departmentDepartment of Biological Science and Technologyen_US
dc.contributor.departmentInstitude of Bioinformatics and Systems Biologyen_US
dc.identifier.wosnumberWOS:000255311500105-
dc.citation.woscount20-
Appears in Collections:Articles


Files in This Item:

  1. 000255311500105.pdf