Complex Systems Division, Beijing Computational Science Research Center, Haidian, Beijing, 100193, China.
School of Software Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.
Sci Rep. 2020 Mar 9;10(1):4371. doi: 10.1038/s41598-020-61205-w.
Amino acids form protein 3D structures in unique manners such that the folded structure is stable and functional under physiological conditions. Non-specific and non-covalent interactions between amino acids exhibit neighborhood preferences. Based on structural information from the protein data bank, a statistical energy function was derived to quantify amino acid neighborhood preferences. The neighborhood of one amino acid is defined by its contacting residues, and the energy function is determined by the neighboring residue types and relative positions. The neighborhood preference of amino acids was exploited to facilitate structural quality assessment, which was implemented in the neighborhood preference program NEPRE. The source codes are available via https://github.com/LiuLab-CSRC/NePre.
氨基酸以独特的方式形成蛋白质的 3D 结构，使得折叠结构在生理条件下稳定且具有功能。氨基酸之间的非特异性和非共价相互作用表现出局部偏好。基于来自蛋白质数据库的结构信息，推导出了一个统计能量函数来量化氨基酸的局部偏好。一个氨基酸的局部由其接触残基定义，能量函数由相邻残基类型和相对位置决定。氨基酸的局部偏好被用来促进结构质量评估，这在局部偏好程序 NEPRE 中得到了实现。源代码可以通过 https://github.com/LiuLab-CSRC/NePre 获得。
