標題: | Protein structure database search and evolutionary classification |
作者: | Yang, Jinn-Moon Tung, Chi-Hua 生物科技學系 生物資訊及系統生物研究所 Department of Biological Science and Technology Institude of Bioinformatics and Systems Biology |
公開日期: | 2006 |
摘要: | 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. |
URI: | http://hdl.handle.net/11536/12817 http://dx.doi.org/10.1093/nar/gkl395 |
ISSN: | 0305-1048 |
DOI: | 10.1093/nar/gkl395 |
期刊: | NUCLEIC ACIDS RESEARCH |
Volume: | 34 |
Issue: | 13 |
起始頁: | 3646 |
結束頁: | 3659 |
顯示於類別: | 期刊論文 |