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Bioinformatics Advance Access originally published online on November 11, 2008
Bioinformatics 2009 25(3):413-414; doi:10.1093/bioinformatics/btn584
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProtorP: a protein–protein interaction analysis server

Christopher Reynolds , David Damerell and Susan Jones *

Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, Brighton BN1 9QG, UK

*To whom correspondence should be addressed.


  Abstract

Summary: The PROTORP server analyses protein–protein associations in 3D structures. The server calculates a series of physical and chemical parameters of the protein interaction sites that contribute to the binding energy of the association. These parameters include, size and shape, intermolecular bonding, residue and atom composition and secondary structure contributions. The server is flexible, in that it allows users to analyse individual protein associations or large datasets of associations deposited in the PDB, or upload and analyse proprietary files. The properties calculated can be compared with parameter distributions for non-homologous datasets of different classes of protein associations provided on the server website. The server provides an efficient way of characterizing protein–protein associations of new or existing proteins, and a means of putting these values in the context of previously observed associations.

Availability: http://www.bioinformatics.sussex.ac.uk/protorp

Contact: s.jones{at}sussex.ac.uk

Associate Editor: Burkhard Rost

Received on July 1, 2008; revised on October 30, 2008; accepted on November 7, 2008

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