Structure-based function inference using protein family-specific fingerprints.

ABSTRACT: We describe a method to assign a protein structure to a functional family using family-specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active-site templates. Fingerprints were derived for 120 families in SCOP using Frequent Subgraph Mining. For a new structure, all occurrences of these family-specific fingerprints may be found by a fast algorithm for subgraph isomorphism; the structure can then be assigned to a family with a confidence value derived from the number of fingerprints found and their distribution in background proteins. In validation experiments, we

SUBMITTER: Bandyopadhyay D 

PROVIDER: S-EPMC2265098 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature