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Open Access Method

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

Chi-Hua Tung1, Jhang-Wei Huang1 and Jinn-Moon Yang123*

Author Affiliations

1 Institute of Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan

2 Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, 30050, Taiwan

3 Core Facility for Structural Bioinformatics, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, Taiwan

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Genome Biology 2007, 8:R31  doi:10.1186/gb-2007-8-3-r31

Published: 3 March 2007

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 (κ, α) 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.