Nucleic Acids Research Advance Access originally published online on May 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W561-W567; doi:10.1093/nar/gkm346
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W561-W567
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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3D-partner: a web server to infer interacting partners and binding models
1Institute of Bioinformatics, National Chiao Tung University, Hsinchu, 30050, Taiwan, 2Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30050, Taiwan and 3Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan
*To whom correspondence should be addressed. Tel: +886-3-571212-56942; Fax: +886-3-579288; Email: moon{at}faculty.nctu.edu.tw, moon{at}cc.nctu.edu.tw
Received February 1, 2007. Revised April 3, 2007. Accepted April 22, 2007.
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 
15 s 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.
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