Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.
复制标题
DOI：
10.1186/1748-7188-2-12
复制
发表时间：
2007-10-03
影响因子：
1
通讯作者：
Pedersen, Anders G
中科院分区：
文献类型：
--
作者：
Gouveia-Oliveira, Rodrigo;Pedersen, Anders G
一些氨基酸残基在功能上相互作用。这种相互作用将导致这些残基之间的进化共同变异-共同进化。我们的目标是找到这些共同进化的残基。我们提出了六种新的方法检测共进化残基。除其他外，我们建议的措施，是互信息的变体，并使用每个残基的多维表示，以捕捉氨基酸之间的物理化学相似性的措施。我们创建了一个基准系统，在硅片上，能够通过广泛的现实条件来评估这些方法。最后，我们使用不同方法的组合作为提高性能的一种方式。我们最好的方法（行和列加权互信息）的估计准确率比互信息提高了63%。此外，我们表明，不同方法的组合是有效的，并且这些方法对测试的不同条件相当敏感。
Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Our goal is to find these coevolving residues. We present six new methods for detecting coevolving residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate these methods through a wide range of realistic conditions. Finally, we use the combination of different methods as a way of improving performance. Our best method (Row and Column Weighed Mutual Information) has an estimated accuracy increase of 63% over Mutual Information. Furthermore, we show that the combination of different methods is efficient, and that the methods are quite sensitive to the different conditions tested.