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Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6559-63. Epub 2004 Apr 15.

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

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  • 1NEC Laboratories America, 4 Independence Way, Princeton, NJ 08540, USA.


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.

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