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Bioinformatics Advance Access published online on September 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm434
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

meta-PPISP: a Meta Web Server for Protein-Protein Interaction Site Prediction

Sanbo Qin 1,2 and Huan-Xiang Zhou 1–3,*

1Institute of Molecular Biophysics and 2School of Computational Science and 3Department of Physics, Florida State University, Tallahassee, Florida 32306, USA.

*To whom correspondence should be addressed. Prof. Huan-Xiang Zhou, E-mail: zhou{at}sb.fsu.edu


  Abstract

Summary: A number of complementary methods have been developed for predicting protein-protein interaction sites. We sought to increase prediction robustness and accuracy by combining results from different predictors, and report here a meta web server, meta-PPISP, that is built on three individual web servers: cons-PPISP (http://pipe.scs.fsu.edu/ppisp.html), Promate (http://bioportal.weizmann.ac.il/promate), and PINUP (http://sparks.informatics.iupui.edu/PINUP/). A linear regression method, using the raw scores of the three servers as input, was trained on a set of 35 nonhomologous proteins. Cross validation showed that meta-PPISP outperforms all the three individual servers. At coverages identical to those of the individual methods, the accuracy of meta-PPISP is higher by 4.8 to 18.2 percentage points. Similar improvements in accuracy are also seen on CAPRI and other targets.

Availability: meta-PPISP can be accessed at http://pipe.scs.fsu.edu/meta-ppisp.html.

Contact: zhou{at}sb.fsu.edu; phone: (850) 645-1336; fax: (850) 644-7244.

Supplementary information: Data sets, linear regression coefficients, and details of prediction results are shown at the site of the meta-PPISP server.

Associate Editor: Prof. Anna Tramontano

Received on May 18, 2007; revised on August 13, 2007; accepted on August 18, 2007

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