Lu Zaixin, Zhao Zhiyu, Garcia Sergio, Krishnaswamy Krishnakumar, Fu Bin
Department of Computer Science, University of Texas-Pan American, Edinburg, TX 78539, USA.
J Bioinform Comput Biol. 2009 Oct;7(5):755-71. doi: 10.1142/s021972000900431x.
We have developed an algorithm and web tool to search similar protein structures in the PDB (Protein Data Bank). The algorithm is a combination of a series of methods including protein classification, geometric feature extraction, sequence alignment, and 3D structure alignment. Given a protein structure, the tool can efficiently discover similar structures from hundreds of thousands of structures stored in the PDB. Our experimental results show that it is more accurate than other well-known protein search systems including PSI-BLAST, 3D-BLAST, and SSM in finding proteins that are structurally similar to the query protein, and its speed is also competitive with those systems. The algorithm has been fully implemented and is accessible online at the address http://fpsa.cs.panam.edu/, which is supported by a cluster of computers.
我们开发了一种算法和网络工具，用于在蛋白质数据库（PDB）中搜索相似的蛋白质结构。该算法是一系列方法的组合，包括蛋白质分类、几何特征提取、序列比对和三维结构比对。给定一个蛋白质结构，该工具能够从PDB中存储的数十万种结构中高效地发现相似结构。我们的实验结果表明，在寻找与查询蛋白质结构相似的蛋白质方面，它比其他知名的蛋白质搜索系统（包括PSI-BLAST、3D-BLAST和SSM）更准确，并且其速度也与这些系统具有竞争力。该算法已完全实现，可通过网址http://fpsa.cs.panam.edu/在线访问，该网站由一组计算机提供支持。
