Improving protein structure similarity searches using domain boundaries based on conserved sequence information.

ABSTRACT:

Background

The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain Database (CDD) would affect the domain comparisons and structure similarity search performance of VAST.

Results

Alternative domains, which have significantly different secondary structure composition from those bas

SUBMITTER: Thompson KE 

PROVIDER: S-EPMC2694201 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature