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1: Genome Biol. 2007;8(3):R31.Click here to read Click here to read Links

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

Tung CH, Huang JW, Yang JM.

Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan. chihuah.bi91g@nctu.edu.tw

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.

PMID: 17335583 [PubMed - indexed for MEDLINE]

PMCID: PMC1868941