SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.

ABSTRACT: Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to pat

SUBMITTER: Nadzirin N 

PROVIDER: S-EPMC3394286 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature