Quantitative analysis of nucleic acid three-dimensional structures
Quantitative analysis of nucleic acid three-dimensional structures
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DOI：
10.1006/jmbi.2001.4626
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发表时间：
2001-05-18
影响因子：
5.6
通讯作者：
Major, F
中科院分区：
文献类型：
--
作者：
Gendron, P;Lemieux, S;Major, F
本文介绍了一种新的计算机注释DNA和RNA三维结构的程序MC-Annotate。注释的目标是有效地提取和处理结构信息，以简化进一步的结构分析和搜索，并客观地表示结构知识。MC-Annotate的输入是PDB格式的DNA或RNA三维结构。MC-Annotate的输出由包含注释的结构图和一系列HTML文档组成，每个文档对应于输入结构中存在的每个核苷酸构象和碱基-碱基相互作用。所有核苷酸的原子坐标和所有碱基-碱基相互作用的齐次变换矩阵存储在结构图中。核苷酸构象的符号分类，使用糖puckering模式和氮碱基周围的糖基键的方向，和碱基-碱基的相互作用，使用堆叠和氢键的信息，进行了介绍。定义了核苷酸构象和碱基相互作用的特异性因子，以表明它们与所有其他例子的边缘性。特殊性因素使我们能够识别不规则区域和可能的立体化学错误的3-D结构，而无需交互式可视化。附加到每个核苷酸构象的注释包括其类别、其扭转角、与同类实例的均方根偏差的分布、同类实例的列表以及其特异性值。附加到每个基-基交互的注释包括它的类、与同类示例的距离分布、同类示例的列表及其特性值。两个齐次变换矩阵之间的距离进行评估，使用一个新的度量，区分旋转和平移的变换矩阵的背景下的氮碱。MC-Annotate用于构建核苷酸构象和碱基-碱基相互作用的数据库。它被应用到核糖体RNA片段，结合蛋白质L11，注释揭示了特殊的核苷酸构象和碱基之间的相互作用的区域中的RNA接触的蛋白质。目前的RNA三维结构数据库是否完整的问题得到解决。(C)北京：科学出版社.
A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the List of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed. (C) 2001 Academic Press.