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Nucleic Acids Research 2006 34(13):3646-3659; doi:10.1093/nar/gkl395
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Published online 2 August 2006

Nucleic Acids Research, 2006, Vol. 34, No. 13 3646-3659
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article

Protein structure database search and evolutionary classification

Jinn-Moon Yang1,2,3,* and Chi-Hua Tung2

1 Department of Biological Science and Technology, National Chiao Tung University Hsinchu, 30050, Taiwan 2 Institute of Bioinformatics, National Chiao Tung University Hsinchu, 30050, Taiwan 3 Core Facility for Structural Bioinformatics, National Chiao Tung University Hsinchu, 30050, Taiwan

*To whom correspondence should be addressed. Tel: 886 3 5712121, ext. 56942; Fax: 886 3 5729288; Email: moon{at}faculty.nctu.edu.tw

Received March 8, 2006. Revised May 6, 2006. Accepted May 9, 2006.

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw]


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