Tung C S, Carter E S
Theoretical Division, Los Alamos National Laboratory, NM 87545.
Comput Appl Biosci. 1994 Jul;10(4):427-33. doi: 10.1093/bioinformatics/10.4.427.
The helical nature of the molecule (almost all of the DNA and a significant portion of the RNA) makes the modeling of nucleic acids a unique task. Unlike other biopolymers (proteins, lipids, etc.), the integrity the structure of a nucleic acid molecule depends strongly on the maintenance of the base pairing within the molecule. Structural alterations (bending, stretching, compressing, etc.), in general, should not disturb the base pairings. A custom-made molecular modeling tool is developed taking into consideration this specific property of the molecule. Instead of Cartesian coordinates, the modeling is carried out on a set of reduced coordinates developed here in our laboratory. One of the advantages using this set of reduced coordinates is the readiness of maintaining the base pairings while altering the structure. A graphic routine is incorporated into the package to display the image of the molecule while the modeling work is being executed. The program is written in C using XView tool kit with Xlib routines to ensure portability to different workstations.
分子（几乎所有的DNA和相当一部分的RNA）的螺旋性质使得核酸建模成为一项独特的任务。与其他生物聚合物（蛋白质、脂质等）不同，核酸分子结构的完整性在很大程度上取决于分子内碱基配对的维持。一般来说，结构改变（弯曲、拉伸、压缩等）不应干扰碱基配对。考虑到分子的这一特殊性质，开发了一种定制的分子建模工具。建模不是基于笛卡尔坐标，而是在我们实验室开发的一组简化坐标上进行。使用这组简化坐标的优点之一是在改变结构时易于维持碱基配对。该软件包中包含一个图形程序，以便在执行建模工作时显示分子图像。该程序用C语言编写，使用XView工具包和Xlib例程，以确保可移植到不同的工作站。
