Toward the detection and validation of repeats in protein structure
Toward the detection and validation of repeats in protein structure
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DOI：
10.1002/prot.20202
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发表时间：
2004-11-01
影响因子：
2.9
通讯作者：
Thornton, JM
中科院分区：
文献类型：
--
作者：
Murray, KB;Taylor, WR;Thornton, JM
我们提出了一种称为DAVROS的方法来检测、定位和验证蛋白质结构中允许插入和删除的重复基序。DAVROS使用来自结构对齐程序（SAP）的分数矩阵，使用基于概念的算法来搜索重复的motif。信号处理和排列的统计特性。该方法在非冗余蛋白质数据库中进行了测试，并为每个链分配了一个分数。在得分排名前50位的链条中，70%包含重复的图案，没有错误。这代表了14种褶皱覆盖物。和蛋白类。第二个数据集包括三磷酸异构酶（TIM）桶、富亮氨酸重复序列（LRR）、三叶草和α - α桶折叠的不同序列家族的蛋白质链，用于评估DAVROS检测特定折叠中所有基元的能力。在第二个测试集中，LRR链的基元检测率最高（88.7%），TIM桶的基元检测率最低（60%）。这种可变性是由于LRR基序与TIM桶的alpha单元相比具有规律性，后者通常具有更多的索引。这些降低了SAP矩阵中重复信号的强度，使得重复检测更加困难。(C) 2004 Wiley-Liss, Inc。
We present a method called DAVROS to detect, localize, and validate repeating motifs in protein structure allowing for insertions and deletions. DAVROS uses the score matrix from a structural alignment program (SAP) to search for repeating motifs using an algorithm based on concepts from. sinal processing and the statistical properties of the alignments. The method was tested against a nonredundant Protein Data Bank, and each chain was assigned a score. For the top 50 chains ranked by score, 70% contain repeating motifs detected without error. These represent 14 types of fold covering. alpha, beta, and alphabeta protein classes. A second data set comprising protein chains in different sequence families for triosephosphate isomerase (TIM) barrel, leucine-rich repeat (LRR), trefoil, and alpha-alpha barrel folds was used to assess the ability of DAVROS to detect all motifs within a specific fold. For the second test set, the percentage of motifs detected was highest for the LRR chains (88.7%) and least for the TIM barrels (60%). This variability results from the regularity of the LRR motif compared to the alphabeta units of the TIM barrel, which generally have many more indels. These reduce the strength of the repeat signal in the SAP matrix, making repeat detection more difficult. (C) 2004 Wiley-Liss, Inc.