Meta-PPISP: A meta web server for protein-protein interaction site prediction

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) 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. © The Author 2007. Published by Oxford University Press. All rights reserved.