Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.

Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan.
Genome biology (Impact Factor: 10.47). 02/2007; 8(3):R31. DOI: 10.1186/gb-2007-8-3-r31
Source: PubMed

ABSTRACT 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, and effective and reliable search capabilities) and employs a kappa-alpha (kappa, alpha) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity.

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