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Updated: Jul 16, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein
Chi-Hua Tung1, Jhang-Wei Huang, Jinn-Moon Yang
1Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan. chihuah.bi91g@nctu.edu.tw
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 (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.
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