LES--NEW METHOD FOR COMPUTER SIMULATIONS OF PROTEINS

这项研究旨在进一步开发一种新计算机的能力 显著增强范围和通用性的模拟技术 通常的分子动力学模拟。三个大方向将是 探索： (I)小肽结构的测定。多肽的结构 (如果存在)具有重大意义。多肽转移 受体的信号和对其构象的研究可能导致 替代品的设计。此外，短肽的结构可以 建议蛋白质折叠过程的起始点。存在 具有独特结构的高概率多肽片段可以 大大加快了折叠过程。 (Ii)提纯低分辨率蛋白质结构。现如今， 基于统计的计算方法的能力 方法正在稳步增加。尽管如此，到目前为止，结构 得到的分辨率都很低。全球“低分辨率”的组合 基于LES的搜索方法和原子细节细化程序是一种 前景看好的方法。 (3)分子动力学时间尺度的扩展。大专院校提供 抽样分子事件的统计数据要多得多。对于动力学 LES是平均场的近似。然而，在二进制碰撞的情况下 由我们开发的大涡模拟定量描述了扩散和 将被用来研究蛋白质基质中的配基逃逸 纳秒时间刻度，一个无法访问的时间刻度 以前的分子动力学。

This research aims to further develop the capabilities of a new computer simulation technique that significantly enhances the scope and versatility of usual molecular dynamics simulations. Three general directions will be explored: (i) Determination of structure of small peptides. Structure of peptides (when existent) are of significant interest. Many peptides transfer signals to receptors and investigation of their conformations may lead to the design of substitutes. Furthermore, structure of short peptides may suggest initiation site for the process of protein folding. Presence of peptide segments with high probability for a unique structure may accelerate considerably the folding process. (ii) Refinement of low resolution protein structure. Nowadays the capabilities of computational methods that are based on statistical approaches are steadily increased. Nevertheless, so far the structure obtained are of low resolution. The combination of "low resolution" global search methods and atomic detail refinement procedures based on LES is a promising approach. (iii) Extension of molecular dynamics time scales. The LES provides considerably more statistics for sampling molecular events. For dynamics LES is a mean field approximation. However, with a binary collision correction developed by us the LES describes diffusion quantitatively and will be employed to study ligand escapes from a protein matrix on the tens of nanoseconds time scale, a time scale that was not accessible to molecular dynamics before.