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
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