Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading
Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading
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DOI：
10.1089/cmb.2011.0307
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发表时间：
2012-07-01
影响因子：
1.7
通讯作者：
Gront, Dominik
中科院分区：
文献类型：
--
作者：
Gniewek, Pawel;Kolinski, Andrzej;Gront, Dominik
蛋白质序列自动比较方法的发展变得越来越重要。比较谱的方法允许使用关于整个蛋白质家族的信息，从而导致更灵敏和更准确地检测远亲序列。在这方面的贡献，我们描述了一个彻底的优化和测试的轮廓到轮廓对齐方法。已经实施了许多不同的评分方案，并根据它们识别来自相同SCOP家族的模板蛋白作为查询的能力进行比较。除了序列图谱外，还使用二级结构图谱来提高成功检测率。我们的研究结果表明，一个适当调整的一维线程的方法可以识别一个正确的模板，从同一个SCOP家庭几乎以及结构对齐。我们的基准集，这可能是有用的，在其他类似的研究，以及我们开发的折叠识别软件可以下载（www.bioshell.pl/profile-alignments）。
The development of automatic approaches for the comparison of protein sequences has become increasingly important. Methods that compare profiles allow for the use of information about whole protein families, resulting in more sensitive and accurate detection of distantly related sequences. In this contribution, we describe a thorough optimization and tests of a profile-to-profile alignment method. A number of different scoring schemes has been implemented and compared on the basis of their ability to identify a template protein from the same SCOP family as a query. In addition to sequence profiles, secondary structure profiles were used to increase the rate of successful detection. Our results show that a properly tuned one-dimensional threading method can recognize a correct template from the same SCOP family nearly as well as structural alignment. Our benchmark set, which might be useful in other similar studies, as well as the fold-recognition software we developed may be downloaded (www.bioshell.pl/profile-alignments).