Caflisch A, Niederer P, Anliker M
Institute of Biomedical Engineering and Medical Informatics, Swiss Federal Institute of Technology, Zürich.
Proteins. 1992 Sep;14(1):102-9. doi: 10.1002/prot.340140111.
A new minimization procedure for the global optimization in cartesian coordinate space of the conformational energy of a polypeptide chain is presented. The Metropolis Monte Carlo minimization is thereby supplemented by a thermalization process, which is initiated whenever a structure becomes trapped in an area containing closely located local minima in the conformational space. The method has been applied to the endogenous opioid pentapeptide methionine enkephalin. Five among 13 different starting conformations led to the same apparent global minimum of an in-house developed energy function, a type II' reverse turn, the central residues of which are Gly-3-Phe-4. A comparison between the ECEPP/2 global minimum conformation of methionine enkephalin and the apparent one achieved by the present method shows that minimum-energy conformations having a certain similarity can be generated by relatively different force fields.
本文提出了一种新的最小化程序，用于在笛卡尔坐标空间中对多肽链构象能量进行全局优化。通过热化过程对Metropolis蒙特卡罗最小化方法进行了补充，每当一种结构被困在构象空间中包含紧密相邻局部最小值的区域时，就会启动热化过程。该方法已应用于内源性阿片五肽甲硫氨酸脑啡肽。13种不同的起始构象中有5种导致了内部开发的能量函数的相同表观全局最小值，即II'型反向转角，其中心残基为Gly-3-Phe-4。甲硫氨酸脑啡肽的ECEPP/2全局最小构象与本方法获得的表观全局最小构象之间的比较表明，相对不同的力场可以生成具有一定相似性的最低能量构象。
