Protein ranking: from local to global structure in the protein
Jason Weston, Andre Elisseef, Dengyong Zhou, Christina Leslie and
William Stafford Noble
Proceedings of the National Academy of Science.
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.