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Nucleic Acids Research Advance Access originally published online on May 6, 2009
Nucleic Acids Research 2009 37(Web Server issue):W519-W525; doi:10.1093/nar/gkp306
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W519-W525
© 2009 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.

Articles

Protinfo PPC: A web server for atomic level prediction of protein complexes

Weerayuth Kittichotirat, Michal Guerquin, Roger E. Bumgarner and Ram Samudrala*

Department of Microbiology, University of Washington, Seattle, WA, USA

*To whom correspondence should be addressed. Tel: +1 206 251 8852; Fax: +1 206 732 6055; Email: ram{at}compbio.washington.edu

Received January 31, 2009. Revised April 7, 2009. Accepted April 15, 2009.

‘Protinfo PPC’ (Prediction of Protein Complex) is a web server that predicts atomic level structures of interacting proteins from their amino-acid sequences. It uses the interolog method to search for experimental protein complex structures that are homologous to the input sequences submitted by a user. These structures are then used as starting templates to generate protein complex models, which are returned to the user in Protein Data Bank format via email. The server supports modeling of both homo and hetero multimers and generally produces full atomic level models (including insertion/deletion regions) of protein complexes as long as at least one putative homologous template for the query sequences is found. The modeling pipeline behind Protinfo PPC has been rigorously benchmarked and proven to produce highly accurate protein complex models. The fully automated all atom comparative modeling service for protein complexes provided by Protinfo PPC server offers wide capabilities ranging from prediction of protein complex interactions to identification of possible interaction sites, which will be useful for researchers studying these topics. The Protinfo PPC web server is available at http://protinfo.compbio.washington.edu/ppc/


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