3D-BLASTand fastSCOP:Structural Genomics

Our paper, Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for fast protein structure database search, was published

In this paper, we present a novel protein structure database search tool, 3D-BLAST , that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, search effective and reliable search capabilities) by using a kappa-alpha (k,a) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches over 12,000 protein structures in 1.2 seconds and yields good results in zones with low sequence similarity. The number of citations is over 30 for these papers from 2006.

fastSCOP (fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies , published in NAR) rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. fastSCOP uses 3D-BLASTto scan quickly a large structural classification database and MAMMOTH, a detailed structural alignment tool, is adopted to refine domain boundaries and to identify evolutionary superfamilies

Protein Structure

We coperate with...