Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
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DOI：
10.1093/bioinformatics/btm604
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发表时间：
2008-02-01
期刊：
影响因子：
5.8
通讯作者：
Gloor, G. B.
中科院分区：
文献类型：
--
作者：
Dunn, S. D.;Wahl, L. M.;Gloor, G. B.
动机：蛋白质家族进化过程中的补偿性改变会产生包含重要结构和功能信息的共同进化位置。然而，一个高的背景组成的随机噪声和系统发育成分干扰识别的coevolving positions.Results：我们已经开发出一种快速，简单和通用的方法，基于信息论，准确地估计在一个给定的蛋白质家族的每对位置的背景互信息的水平。去除这一背景的结果在一个度量，MIp，正确地识别实质上更多的蛋白质家族中的共同进化的位置比任何现有的方法。这些位置的一个显着的一小部分共同进化强烈的一个或只有少数几个位置。绝大多数这样的位置对在代表性结构中是接触的。强共同进化的位置对的识别可以用来施加显着的结构限制，应该是从头开始蛋白质折叠的一个重要的附加约束。
Motivation: Compensating alterations during the evolution of protein families give rise to coevolving positions that contain important structural and functional information. However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions.Results: We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Removal of this background results in a metric, MIp, that correctly identifies substantially more coevolving positions in protein families than any existing method. A significant fraction of these positions coevolve strongly with one or only a few positions. The vast majority of such position pairs are in contact in representative structures. The identification of strongly coevolving position pairs can be used to impose significant structural limitations and should be an important additional constraint for ab initio protein folding.