CLePAPS：基于构象字母的蛋白质结构快速配对
CLePAPS: Fast Pair Alignment of Protein Structures Based on Conformational Letters
摘要：
快速、高效、可靠的蛋白质结构两两比对算法在分析快速增长的蛋白质结构数据中的需求越来越大。CLePAPS是为此目的开发的工具。它区别于其他现有的算法通过使用构象字母，这是离散状态的3D片段结构状态。字母对应于由四个连续残基的C_alpha假键形成的三个角的组合的簇。一个名为CLESUM的替代矩阵可用于测量任何两个此类字母之间的相似性。CLePAPS将对齐片段对（AFP）视为具有高的成对CLESUM分数之和的无帽字符串对。使用CLESUM分数作为相似性度量，CLePAPS通过简单的字符串比较来搜索AFP。最好地叠加高度相似的AFP的变换可以用于在比较中对结构对进行分类。与几种其他AFP一致的高评分AFP确定初始比对。然后，CLePAPS加入一致的AFP，由它们的相似性分数指导，通过几个“放大”迭代步骤来扩展比对。后续的细化产生最终的对齐。CLePAPS不实现动态编程。在各种蛋白质结构对上测试CLePAPS的效用。
英文摘要：
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes itself from other existing algorithms by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of the three angles formed by C_alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure similarity between any two such letters. CLePAPS regards an aligned fragment pair (AFP) as an ungapped string pair with a high sum of pairwise CLESUM scores. Using CLESUM scores as the similarity measure, CLePAPS searches for AFPs by simple string comparison. The transformation which best superimposes a highly similar AFP can be used to superimpose the structure pairs under comparison. A highly scored AFP which is consistent with several other AFPs determines an initial alignment. CLePAPS then joins consistent AFPs guided by their similarity scores to extend the alignment by several `zoom-in' iteration steps. A follow-up refinement produces the final alignment. CLePAPS does not implement dynamic programming. The utility of CLePAPS is tested on various protein structure pairs.
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