FPOP: footprinting functional pockets of proteins by comparative spatial patterns.

ABSTRACT: fPOP (footprinting Pockets Of Proteins, http://pocket.uchicago.edu/fpop/) is a relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. We previously used a purely geometric method to extract the spatial patterns of functional surfaces (split pockets) in approximately 19,000 bound structures and constructed a database, SplitPocket (http://pocket.uchicago.edu/). These functional surfaces are now used as spatial templates to predict the binding surfaces of unbound structures. To conduct a shape comparison, we use the Smith-Waterman algorithm to footprint an unbound pocket fragment with those of the functional surfaces in SplitPocket. The pairwise alignment of the unbound a

SUBMITTER: Tseng YY 

PROVIDER: S-EPMC2808891 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature