3D representations of amino acids-applications to protein sequence comparison and classification.
3D representations of amino acids-applications to protein sequence comparison and classification.
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DOI：
10.1016/j.csbj.2014.09.001
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发表时间：
2014-08
影响因子：
6
通讯作者：
Koehl, Patrice
中科院分区：
文献类型：
--
作者：
Li, Jie;Koehl, Patrice
蛋白质的氨基酸序列是了解其结构并最终了解其在细胞中的功能的关键。本文讨论了编码氨基酸的基本问题，即这样的蛋白质序列的表示有助于对其信息内容的解码。我们表明，从氨基酸替代矩阵得到的三维(3D)空间中的基于特征的表示提供了一个足够的表示，可以用于基于几何的蛋白质序列的直接比较。我们在蛋白质结构折叠预测问题的背景下衡量这种表示的性能。我们将属于不同结构折叠的不同蛋白质组的分类结果与从序列单独或直接从结构信息获得的相同蛋白质的分类进行比较。我们发现，序列本身作为结构分类器的性能很差。相反，我们表明，使用序列的三维表示显著提高了分类精度。最后，我们讨论了这种表述目前的局限性，并对可能的改进进行了说明。
The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acids in ways that the representation of such a protein sequence facilitates the decoding of its information content. We show that a feature-based representation in a three-dimensional (3D) space derived from amino acid substitution matrices provides an adequate representation that can be used for direct comparison of protein sequences based on geometry. We measure the performance of such a representation in the context of the protein structural fold prediction problem. We compare the results of classifying different sets of proteins belonging to distinct structural folds against classifications of the same proteins obtained from sequence alone or directly from structural information. We find that sequence alone performs poorly as a structure classifier. We show in contrast that the use of the three dimensional representation of the sequences significantly improves the classification accuracy. We conclude with a discussion of the current limitations of such a representation and with a description of potential improvements.