Development of a System of Simulation Biopolymer Systems in Dihedral Angle Space

在过去的十几年里，我们一直在开发一个计算系统和一个软件系统来实现生物聚合物体系在二面角空间中的构象模拟计算。该项目的目的是(A)扩大这一计算的范围和(B)准备将其提供给世界各地的用户。为了达到这些目的，我们取得了以下成果。(1)根据算法所蕴含的内在逻辑，对软件系统进行了重构。从而达到了系统的通用性和灵活性。描述这种重新表述的一篇论文发表在《计算机物理通信》杂志上。(2)二面角空间的计算系统在蛋白质中的应用是非常成功的。然而，五元核糖和脱氧核糖环的灵活性阻碍了核酸的成功应用。为了克服这一困难，必须发展一种分析理论来处理核糖环和脱氧核糖环的假旋转。我们已经成功地从根本上解决了这个问题。一篇描述这一理论的文章发表在《物理化学杂志》上。(3)结合上述处理五元环的假转动的方法，我们发展了一套处理核酸的计算系统。更具体地说，我们开发了一种算法，可以从实验核磁共振信息中获得的距离信息来推断核酸的三维结构。这种算法可以精确地处理核糖环和脱氧核糖环的柔韧性。与目前流行的笛卡尔坐标空间算法相比，该算法不仅速度更快，而且偏差更小。

During the last ten or more years we have been developing a system of computation and a software system to implement the computation for simulation of conformations of biopolymer systems in the dihedral angle space. The purpose of this project is (a) to expand the scope of this computation and (b) to prepare for making it available for world-wide users. As to these purposes we have attained the following results. (1) The system of software has been reformulated according to the intrinsic logic which the algorithm contains inherently. Accordingly the system attained a generality and flexibility. A paper describing this reformulation is in press in Computer Physics Communication. (2) The system of computation in the dihedral angle space has proved very successful as applied for proteins. However, successful application for nucleic acids has been hampered by the flexibilities of the five-memebered ribose and deoxyribose rings. In order to overcome this difficulty, an analytic theory to treat pseudo-rotation of ribose and deoxyribose rings has to be developed. We have succeeded to give a fundamental solution to this problem. A peper describing this theory has been published in J.Phys.Chem. (3) We have developed a system of computation for treating nucleic acids by incorporating the above method of treating the pseudo-rotation of the five-membered rings. To be more specific, we have developed an algorithm to deduce three dimensional strucutres of nucleic acids from distance information obtainable from experimental NMR information. This algorithm allows to treat accurately the flexibities of ribose and deoxyribose rings. This algorithm is not only faster but also less biased than the now popular algorithm that works in the Cartesian coordinate space.