Automatic generation and evaluation of sparse protein signatures for families of protein structural domains.

ABSTRACT: We identified key residues from the structural alignment of families of protein domains from SCOP which we represented in the form of sparse protein signatures. A signature-generating algorithm (SigGen) was developed and used to automatically identify key residues based on several structural and sequence-based criteria. The capacity of the signatures to detect related sequences from the SWISSPROT database was assessed by receiver operator characteristic (ROC) analysis and jack-knife testing. Test signatures for families from each of the main SCOP classes are described in relation to the quality of the structural alignments, the SigGen parameters used, and their diagnostic performance. We show that automatically generated signatures are potently diagnostic for their family (ROC50 scores typ

SUBMITTER: Blades MJ 

PROVIDER: S-EPMC2253312 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature