Comparison of sequence and structure alignments for protein domains
Comparison of sequence and structure alignments for protein domains
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DOI：
10.1002/prot.10163
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发表时间：
2002-08-15
影响因子：
2.9
通讯作者：
Bryant, SH
中科院分区：
文献类型：
--
作者：
Marchler-Bauer, A;Panchenko, AR;Bryant, SH
基于蛋白质结构域比对的图谱搜索方法已被证明是比较序列分析中有用的工具。目前可用的搜索方法所使用的结构域比对已经通过序列比较来计算。然而，随着蛋白质结构数据库的增长，许多结构域对的比对也通过结构比较来计算。在这里，我们检查的程度，从这两个来源的信息一致。我们测量的协议，在每个蛋白质中的同源区域的识别，也就是说，相对于域边界的位置。我们还通过比较比对和评估其预测的分子模型的准确性来衡量同源残基位点识别的一致性。我们发现，在公开的集合的基础上的序列和结构比较的结构域比对在很大程度上是一致的。然而，通过序列比较鉴定的同源区域通常比通过3D结构比较鉴定的同源区域短。此外，当整体序列相似性低时，来自序列比较的比对产生不太准确的分子模型，表明它们不太准确地鉴定同源位点。这些观察结果表明，结构比较的结果可能会被用来提高整体精度的域对齐收集和性能的配置文件搜索方法的基础上。
Profile search methods based on protein domain alignments have proven to be useful tools in comparative sequence analysis. Domain alignments used by currently available search methods have been computed by sequence comparison. With the growth of the protein structure database, however, alignments of many domain pairs have also been computed by structure comparison. Here, we examine the extent to which information from these two sources agrees. We measure agreement with respect to identification of homologous regions in each protein, that is, with respect to the location of domain boundaries. We also measure agreement with respect to identification of homologous residue sites by comparing alignments and assessing the accuracy of the molecular models they predict. We find that domain alignments in publicly available collections based on sequence and structure comparison are largely consistent. However, the homologous regions identified by sequence comparison are often shorter than those identified by 3D structure comparison. In addition, when overall sequence similarity is low alignments from sequence comparison produce less accurate molecular models, suggesting that they less accurately identify homologous sites. These observations suggest that structure comparison results might be used to improve the overall accuracy of domain alignment collections and the performance of profile search methods based on them.