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

ABSTRACT: 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 struct

SUBMITTER: Binkowski TA 

PROVIDER: S-EPMC441528 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature