NEW OPTIMIZATION METHOD AND ITS APPLICATION TO COLLAGEN PACKING

(a)胶原蛋白样分子包装的计算研究 胶原蛋白样分子的横向堆积已经通过以下方法进行了检查： 能量最小化与ECEPP/3力场。 双流填料 模型中，Smith胶原微纤维扭曲成等边五边形 模型和准六方堆积模型，已经被广泛地 研究了 准六方堆积结构被发现是 在能量上比史密斯微纤维更有利， 31.2 kcal/mol的五个三重螺旋。 (b)新的优化方法 多肽的构象能计算：构象 空间退火：提出了一种新的优化方法， 多肽的全局最小能量构象。 它结合 构建过程和遗传算法的基本方面， 介绍了构象空间的重要概念 退火 在测试甲硫氨酸脑啡肽时， 问题，得到了公认的全局最小能量构象 对于所有100次独立运行，在约2600次局部最小化后， 指数. 该算法非常适合并行计算， 并且算法的并行化正在进行中，这将 使研究更大的多肽成为可能。

(a) Computational study of packing a collagen-like molecule: The lateral packing of a collagen-like molecule has been examined by energy minimization with the ECEPP/3 force field. Two current packing models, the Smith collagen microfibril twisted equilateral pentagon model and the quasi-hexagonal packing model, have been extensively investigated. The quasi-hexagonal packing structure is found to be energetically more favorable than the Smith microfibril by as much as 31.2 kcal/mol of five triple helices. (b) New optimization method for conformational energy calculations on polypeptides: Conformational space annealing: A new optimization method is presented to search for the global minimum-energy conformations of polypeptides. It combines essential aspects of the build-up procedure and the genetic algorithm, and it introduces the important concept of conformational space annealing. When tested on Met-enkephalin, a 24-dihedral angle problem, the accepted global minimum-energy conformation is obtained for all 100 independent runs after about 2600 local minimizations on average. The algorithm is ideally suited for parallel computations, and the parallelization of the algorithm is in progress, which would make it possible to investigate larger polypeptides.