Computer Science and Information Engineering College, Tianjin University of Science and Technology, Tianjin, 300222, China.
Amino Acids. 2010 Jul;39(2):417-25. doi: 10.1007/s00726-009-0457-y. Epub 2010 Feb 2.
Protein structure alignment algorithms play an important role in the studies of protein structure and function. In this paper, a novel approach for structure alignment is presented. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring geometrically compatible aligned fragment pairs. The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments. We show the superior performance of the proposed algorithm by the computational experiments on several benchmark datasets and the comparisons with the well-known structure alignment algorithms such as DALI, CE and MATT. The proposed method can obtain accurate and biologically significant alignment results for the case with occurrence of internal repeats or indels, identify the circular permutations, and reveal conserved functional sites. A ranking criterion of our algorithm for fold similarity is presented and found to be comparable or superior to the Z-score of CE in most cases from the numerical experiments. The software and supplementary data of computational results are available at http://zhangroup.aporc.org/bioinfo/SANA.
蛋白质结构比对算法在蛋白质结构和功能研究中起着重要的作用。在本文中，提出了一种新的结构比对方法。具体来说，首先通过识别几何相容的相邻片段对网络中的连通分量来对齐两个蛋白质结构的核心区域。然后通过多目标优化方法对初始比对进行细化。该算法可以产生序列和非序列比对。我们通过几个基准数据集上的计算实验以及与 DALI、CE 和 MATT 等著名结构比对算法的比较，展示了所提出算法的优越性能。对于存在内部重复或插入缺失的情况，该方法可以获得准确且具有生物学意义的比对结果，识别环状排列，并揭示保守的功能位点。我们还提出了一种用于折叠相似性的算法排序标准，并在大多数情况下发现它与 CE 的 Z 值相当或优于从数值实验。软件和计算结果的补充数据可在 http://zhangroup.aporc.org/bioinfo/SANA 上获得。
