Xu J, Weber P L, Borer P N
TRIPOS, Inc., St. Louis, MO 63144.
J Biomol NMR. 1995 Feb;5(2):183-92. doi: 10.1007/BF00208809.
A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (approximately 20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.
本文介绍了一个全面的肽段归属程序及其在环孢菌素A这种环肽上的应用。借助环孢菌素A的实例，讨论了一组使用模糊逻辑的图论算法。这些算法可处理严重重叠的峰，恢复不连续和扭曲的自旋耦合网络，并包含序列特异性归属的策略。还介绍了一种扩展蛋白质知识库以自动归属非标准氨基酸残基的程序。该程序能够对小肽（约20个残基）进行完全自动化归属。对于此类分子，肽链是环状还是非环状以及是否存在酰胺质子均不影响其归属。对于较大的肽/蛋白质，则需要更多用户交互，并且序列特异性归属步骤通常必须通过小于全长的片段进行，以避免由于组合爆炸的出现而产生问题。该程序可作为严格的工具来检查人工归属。程序中内置的模糊图论概念通过一个肽段的二维质子谱进行了说明，但可扩展到更高维谱、其他生物聚合物、天然产物和其他有机结构。
