PASCAL - Pattern Analysis, Statistical Modelling and Computational Learning

Protein ranking: from local to global structure in the protein similarity network
Jason Weston, Andre Elisseeff, Dengyong Zhou, Christina S. Leslie and William Stafford Noble
Proceedings of the National Academy of Science Volume 101, Number 17, pp. 6559-6563, 2004.


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.

EPrint Type:Article
Project Keyword:Project Keyword UNSPECIFIED
Subjects:Theory & Algorithms
ID Code:483
Deposited By:Dengyong Zhou
Deposited On:23 December 2004