Protein ranking: from local to global structure in the protein similarity network.

ABSTRACT: Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a precomputed, weighted network. The resulting ranking algorithm, evaluated by using a human-curated database of protein structures, is efficient and provides significantly better rankings than a local network search algorithm such as psi-blast.

SUBMITTER: Weston J 

PROVIDER: S-EPMC404084 | biostudies-literature | 2004 Apr

REPOSITORIES: biostudies-literature