Rapid detection of similarity in protein structure and function through contact metric distances.

ABSTRACT: The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class of computational solutions to this problem is based on the similarity of protein structure. Here, we implement a simple yet efficient measure of protein structure similarity, the contact metric. Even though its computation avoids structural alignments and is therefore nearly instantaneous, we find that small values correlate with geometrical root mean square deviations obtained from structural alignments. To test whether the contact metric detects functional similarity, as defined by Gene Ontology (GO) terms, it was compared in large-scale computational experiments to four other measures of structural similarity, including alignment algorithms as we

SUBMITTER: Lisewski AM 

PROVIDER: S-EPMC1702494 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature