Protein ranking: from local to global structure in the protein similarity network.
basic_science · Level V
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- Record sourced from PubMed, PMID 15087500.
- Also identified by PMC identifier 404084.
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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.
Medical subject headings
- Proteins