Protein ranking: from local to global structure in the protein similarity network -- Supplementary data

Jason Weston, Andre Elisseeff, Dengyong Zhou, Christina Leslie and William Stafford Noble


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 pre-computed, weighted network. The resulting ranking algorithm, evaluated 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.