MOLECULAR STRUCTURE ALIGNMENT SOFTWARE DEVELOPMENT

相关分子的结构比较是一个重要的工具 来理解蛋白质的结构和功能。 几个结构 在文献中已经报道了比较技术（例如， 泰勒和奥伦戈，霍尔姆和桑德，法利科夫和科恩，戈兹克和 Skolnick）。 这些方法中的每一种都定义了其自己的分子度量。 相似性，需要某种类型的用户可定义参数， 生成单一对齐。 虽然这些方法有许多优点， 在这些方法中使用的不同度量可能难以 定量解释，特别是当一个人改变了 用户可定义的参数值。 我们在调查一个 仅使用均方根距离（RMSD）作为 分子相似性度量 而不是产生一个单一的 答案是，对齐是针对不同数量的匹配而产生的 残基 在最简单的分析中，用户可以检查 最大RMSD或最小RMSD的匹配残基数 当匹配固定数目的残基时。 因为结果 可以比较不同分子的距离测量、排列。 一个算法，使用我们的简单的度量已经实现。 的 程序采用刚体变换生成候选 比对和动态编程来对每个候选人进行评分。 的 对于每个匹配残基数目具有最低RMSD的候选者是 以图形方式报告（作为MidasPlus或Chimera图形对象） 和文本（作为多序列格式文件）。 我们目前正在 评估我们的算法对结果的性能 在文献中有报道。

Structural comparison of related molecules is an important tool for understanding protein structure and function. Several structural comparison techniques have been reported in the literature (e.g., Taylor and Orengo, Holm and Sander, Falicov and Cohen, Godzik and Skolnick). Each of these methods defines its own metric of molecular similarity, requires some type of user-definable parameter, and generates a single alignment. While these methods have many merits, the different metrics used in the methods may be difficult to interpret quantitatively, particularly when one varies the user-definable parameter values. We are investigating a structure alignment method which uses only root- mean-square distance (RMSD) as the molecular similarity metric. Rather than generating a single answer, alignments are produced for varying number of matching residues. In the simplest analysis, users can examine the maximum number of matching residues for a maximum RMSD, or the minimum RMSD when matching a fixed number of residues. Because the results are distance measures, alignments of different molecules may be compared. An algorithm that uses our simple metric has been implemented. The program employs rigid body transformations generate candidate alignments nd dynamic programming to score each candidate. The candidate with the lowest RMSD for each number of matching residues is reported, both graphically (as a MidasPlus or Chimera graphics object) and textually (as a Multiple Sequence Format file). We are currently evaluating the performance of our algorithm against the results reported in the literature.