AB INITIO PROTEIN TERTIARY STRUCTURE PREDICTION

(A)包装类胶原蛋白分子的计算研究： 一种胶原样分子的侧向堆积已经通过 ECEPP/3力场下的能量最小化。两种电流填料 模型，史密斯胶原蛋白微丝扭曲等边五边形 模型和准六角堆积模型，得到了广泛的应用 调查过了。发现准六方堆积结构为 在能量上比史密斯微纤丝更有利 5个三螺旋31.2千卡/摩尔。(B)新的优化方法 多肽的构象能计算：构象 空间退火法：一种新的搜索优化方法 多肽的全局最小能量构象。它结合了 积木程序和遗传算法的基本方面， 并引入了构象空间的重要概念 退火法。当测试甲硫氨酸脑啡肽时，24个二面角 问题，得到了公认的全局最小能量构象。 在进行了大约2600次局部最小化之后，对于所有100次独立运行 平均水平。该算法非常适合并行计算， 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.