†Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
‡State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
J Chem Inf Model. 2015 Jun 22;55(6):1261-70. doi: 10.1021/ci500577m. Epub 2015 May 18.
The composition and sequence order of amino acid residues are the two most important characteristics to describe a protein sequence. Graphical representations facilitate visualization of biological sequences and produce biologically useful numerical descriptors. In this paper, we propose a novel cylindrical representation by placing the 20 amino acid residue types in a circle and sequence positions along the z axis. This representation allows visualization of the composition and sequence order of amino acids at the same time. Ten numerical descriptors and one weighted numerical descriptor have been developed to quantitatively describe intrinsic properties of protein sequences on the basis of the cylindrical model. Their applications to similarity/dissimilarity analysis of nine ND5 proteins indicated that these numerical descriptors are more effective than several classical numerical matrices. Thus, the cylindrical representation obtained here provides a new useful tool for visualizing and charactering protein sequences. An online server is available at http://biophy.dzu.edu.cn:8080/CNumD/input.jsp .
氨基酸残基的组成和序列顺序是描述蛋白质序列的两个最重要的特征。图形表示法有助于可视化生物序列，并生成具有生物学意义的数值描述符。在本文中，我们通过将 20 种氨基酸残基类型放置在一个圆内，并将序列位置沿 z 轴排列，提出了一种新颖的圆柱表示法。这种表示法允许同时可视化氨基酸的组成和序列顺序。基于圆柱模型，我们开发了 10 个数值描述符和 1 个加权数值描述符，以定量描述蛋白质序列的固有性质。将这些数值描述符应用于 9 个 ND5 蛋白的相似性/相异性分析表明，这些数值描述符比几种经典的数值矩阵更有效。因此，这里获得的圆柱表示法为可视化和描述蛋白质序列提供了一种新的有用工具。在线服务器可在 http://biophy.dzu.edu.cn:8080/CNumD/input.jsp 访问。
