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Nucleic Acids Research Advance Access published online on April 17, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn181
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© 2008 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.

Web Server

webPIPSA: a web server for the comparison of protein interaction properties

Stefan Richter1,*, Anne Wenzel1, Matthias Stein1, Razif R. Gabdoulline1,2 and Rebecca C. Wade1

1Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss-Wolfsbrunnenweg 33, 69118 and 2BIOMS (Center for Modeling and Simulation in the Biosciences), University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany

*To whom correspondence should be addressed. Tel: +49 6221 533 279; Fax: +49 6221 533 298; Email: stefan.richter{at}eml-r.villa-bosch.de

Received January 31, 2008. Revised March 19, 2008. Accepted March 28, 2008.

Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org.


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