3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
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DOI：
10.1093/nar/gkg680
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发表时间：
2003-09-01
影响因子：
14.9
通讯作者：
Olson, WK
中科院分区：
文献类型：
--
作者：
Lu, XJ;Olson, WK
我们提出了一个全面的软件包，3DNA，用于分析，重建和可视化的三维核酸结构。从蛋白质数据库(PDB)格式的坐标文件开始，3DNA可以处理DNA和RNA结构中存在的反平行和平行双螺旋、单链结构、三链、四链和其他复杂的三级折叠基序。分析程序对所有碱基相互作用进行鉴定和分类，并对适当碱基对步骤的双螺旋特征进行分类。该程序利用最近推荐的用于描述核酸碱基对几何形状的参照系和严格的基于矩阵的方案来计算局部构象参数并根据这些参数重建结构。重建程序产生了核酸的矩形方块表示，以及带有糖-磷酸主干的全原子模型和出版质量的“标准化”基础堆叠图。提供了实用程序来定位结构中的碱基对和螺旋区域，并重新定向结构以实现有效的可视化。基于各种重复序列的X射线衍射测量的常规螺旋模型也可以在该程序中生成。
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.