pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
Department of Bioengineering, The University of Illinois at Chicago, Chicago, IL 60607-7052, USA
* To whom correspondence should be addressed. Tel: +1 312 355 1789; Fax: +1 312 996 5921; Email: jliang{at}uic.edu
Received February 11, 2004; Revised and Accepted March 24, 2004
Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino acid Residues) provides an online resource to identify similar protein surface regions. pvSOAR can take a structure either uploaded by a user or obtained from the Protein Data Bank, and identifies similar surface patterns based on geometrically defined pockets and voids. It provides several search modes to compare protein surfaces by similarity in local sequence, local shape and local orientation. Statistically significant search results are reported for visualization and interactive exploration. pvSOAR can be used to predict biological functions of proteins with known three-dimensional structures but unknown biological roles. It can also be used to study functional relationship between proteins and for exploration of the evolutionary origins of structural elements important for protein function. We present an example using pvSOAR to explore the biological roles of a protein whose structure was solved by the structural genomics project. The pvSOAR web server is available at http://pvsoar.bioengr.uic.edu/.
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