Bansal M, Bhattacharyya D, Ravi B
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Comput Appl Biosci. 1995 Jun;11(3):281-7. doi: 10.1093/bioinformatics/11.3.281.
Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures.
介绍了软件包NUPARM和NUCGEN，它们可通过分析和生成非均匀结构来理解核酸中序列导向的结构变异。定义了一组局部碱基对间参数（即倾斜、滚动、扭曲、位移、滑动和上升），这些参数仅使用两个连续碱基对的几何形状和坐标，可用于为16种可能的二核苷酸步长中的每一种生成具有不同几何形状的聚合物结构。如果需要，碱基对内参数、螺旋桨、扣环、开口和C6...C8距离也可以变化，而在每个核苷酸中，糖磷酸骨架原子以某种标准构象固定。NUPARM可用于分析DNA和RNA结构，包括单链和双链螺旋。NUCGEN软件生成双链螺旋模型，其骨架固定为B型DNA，但通过对输入数据进行适当修改，它也可以生成A型DNA和RNA双链结构。
