標題: 3D-partner: a web server to infer interacting partners and binding models
作者: Chen, Yung-Chiang
Lo, Yu-Shu
Hsu, Wen-Chang
Yang, Jinn-Moon
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 1-Jul-2007
摘要: The 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.
URI: http://dx.doi.org/10.1093/nar/gkm346
http://hdl.handle.net/11536/10619
ISSN: 0305-1048
DOI: 10.1093/nar/gkm346
期刊: NUCLEIC ACIDS RESEARCH
Volume: 35
Issue: 
起始頁: W561
結束頁: W567
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