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

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.