Lu Xiang-Jun, Olson Wilma K
Department of Chemistry and Chemical Biology, Wright-Rieman Laboratories, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
Nucleic Acids Res. 2003 Sep 1;31(17):5108-21. doi: 10.1093/nar/gkg680.
We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.
我们展示了一个用于三维核酸结构分析、重建和可视化的综合软件包——3DNA。从蛋白质数据库（PDB）格式的坐标文件开始，3DNA可以处理反平行和平行双螺旋、单链结构、三链体、四链体以及在DNA和RNA结构中发现的其他复杂三级折叠基序。分析程序可识别并分类所有碱基相互作用，并对合适碱基对步的双螺旋特征进行分类。该程序使用最近推荐的参考系来描述核酸碱基对几何结构，并采用基于矩阵的严格方案来计算局部构象参数，并根据这些参数重建结构。重建程序可生成核酸的矩形块表示以及带有糖磷酸骨架和具有出版质量的“标准化”碱基堆积图的完整原子模型。还提供了实用程序来定位结构中的碱基对和螺旋区域，并重新定向结构以进行有效的可视化。基于各种重复序列的X射线衍射测量的规则螺旋模型也可以在该程序中生成。
