Tung Chi-Hua, Huang Jhang-Wei, Yang Jinn-Moon
Institute of Bioinformatics, National Chiao Tung University, Hsinchu, Taiwan.
Genome Biol. 2007;8(3):R31. doi: 10.1186/gb-2007-8-3-r31.
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.
我们展示了一种新型蛋白质结构数据库搜索工具3D-BLAST，它对于分析新结构很有用，并且可以返回一个排序的比对列表。该工具具有BLAST的特点（例如，强大的统计基础以及有效且可靠的搜索能力），并采用了基于kappa-alpha（κ，α）图推导的结构字母表和一种新的替换矩阵。3D-BLAST在1.2秒内搜索超过12,000个蛋白质结构，并在低序列相似性区域产生良好结果。
