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.
Tung
Chi-Hua
CH
Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan. chihuah.bi91g@nctu.edu.tw
Huang
Jhang-Wei
JW
Yang
Jinn-Moon
JM
D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D016415:Sequence Alignment; D012984:Software