Xie Lei, Bourne Philip E
San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5441-6. doi: 10.1073/pnas.0704422105. Epub 2008 Apr 2.
Here, a scalable, accurate, reliable, and robust protein functional site comparison algorithm is presented. The key components of the algorithm consist of a reduced representation of the protein structure and a sequence order-independent profile-profile alignment (SOIPPA). We show that SOIPPA is able to detect distant evolutionary relationships in cases where both a global sequence and structure relationship remains obscure. Results suggest evolutionary relationships across several previously evolutionary distinct protein structure superfamilies. SOIPPA, along with an increased coverage of protein fold space afforded by the structural genomics initiative, can be used to further test the notion that fold space is continuous rather than discrete.
本文提出了一种可扩展、准确、可靠且稳健的蛋白质功能位点比较算法。该算法的关键组成部分包括蛋白质结构的简化表示以及与序列顺序无关的profile-profile比对（SOIPPA）。我们表明，在全局序列和结构关系仍不明确的情况下，SOIPPA能够检测到远缘进化关系。结果表明了跨越几个先前在进化上不同的蛋白质结构超家族的进化关系。SOIPPA，连同结构基因组学计划所提供的蛋白质折叠空间覆盖率的提高，可用于进一步检验折叠空间是连续而非离散的这一概念。
