Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
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DOI：
10.1093/protein/11.9.739
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发表时间：
1998-09-01
期刊：
影响因子：
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通讯作者：
Bourne, PE
中科院分区：
文献类型：
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作者：
Shindyalov, IN;Bourne, PE
报道了一种新算法，该算法在两个蛋白质结构之间建立了对齐。该算法涉及由对齐片段对（AFP）定义的对齐路径的组合扩展（CE），而不是使用动态编程和蒙特卡洛优化的更传统的技术。顾名思义，AFP是碎片对，每种蛋白质中的一个碎片，它赋予结构相似性。 AFP基于局部几何形状，而不是全球特征，例如二级结构的方向和整体拓扑。代表可能连续比对路径的AFP的组合被选择性扩展或丢弃，从而导致单个最佳比对。该算法可以快速，准确地找到最佳结构对齐，因此适用于数据库扫描和大型蛋白质家族的详细分析。该方法已经过测试并与DALI和DALS的结果进行了比较，并使用了相似结构的代表性样本进行了比较，这些方法未检测到这些其他方法未检测到的几种新结构相似性。可以通过网络http://cl.sdsc.edu/ce.html通过Web执行特定的一对一对准和针对所有结构的搜索。
A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs (AFPs) rather than the more conventional techniques using dynamic programming and Monte Carlo optimization. AFPs, as the name suggests, are pairs of fragments, one from each protein, which confer structure similarity. AFPs are based on local geometry, rather than global features such as orientation of secondary structures and overall topology. Combinations of AFPs that represent possible continuous alignment paths are selectively extended or discarded thereby leading to a single optimal alignment. The algorithm is fast and accurate in finding an optimal structure alignment and hence suitable for database scanning and detailed analysis of large protein families. The method has been tested and compared with results from Dali and VAST using a representative sample of similar structures, Several new structural similarities not detected by these other methods are reported. Specific one-on-one alignments and searches against all structures as found in the Protein Data Bank (PDB) can be performed via the Web at http://cl.sdsc.edu/ce.html.