Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
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ABSTRACT:
SUBMITTER: Tung CH
PROVIDER: S-EPMC1868941 | biostudies-literature | 2007
REPOSITORIES: biostudies-literature
Publications
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
Tung Chi-Hua CH Huang Jhang-Wei JW Yang Jinn-Moon JM
Genome biology 20070101 3
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 sequenc ...[more]
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