pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins

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 t...

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Bibliographic Details
Published in:Nucleic acids research 2004-07, Vol.32 (suppl-2), p.W555-W558
Main Authors: Binkowski, T. Andrew, Freeman, Patrick, Liang, Jie
Format: Article
Language:English
Subjects:
Amino Acids - chemistry
Binding Sites
Databases, Protein
Internet
Models, Molecular
Protein Conformation
Proteins - chemistry
Proteins - metabolism
Proteins - physiology
Software
User-Computer Interface
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Summary: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/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkh390