Martinez Hugo M, Maizel Jacob V, Shapiro Bruce A
Center for Cancer Research Nanobiology Program National Cancer Institute, Building 469, Room 150, Frederick, MD 21702, USA.
J Biomol Struct Dyn. 2008 Jun;25(6):669-83. doi: 10.1080/07391102.2008.10531240.
Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.
利用RNA分子的一级和二级结构信息，RNA2D3D程序能自动且快速地生成与该信息一致的三维构象的一阶近似。它适用于任意分支复杂度和假结含量的结构，其特点是具有高效的交互式图形编辑功能，可消除初始生成过程中引入的任何重叠，并进行有利于目标特征和后续优化的构象变化。该程序着重于对替代三维构象的快速探索，用户可以交互式地添加或删除碱基对，相邻的茎可以同轴堆积或解堆积，单链可以塑形以适应特殊约束，任意子集可以定义并作为刚体进行操作。压缩功能可将茎内的碱基堆积最佳地扩展到连接单链中，这也是使结构更紧凑并揭示折叠基序的一种策略手段。一阶近似的后续优化、修饰以及施加三级约束可借助标准能量优化技术来辅助进行。分子先前确定的任何部分的坐标都能轻松纳入，并且建模结构的任何部分都可以输出为PDB或XYZ文件。文中还展示了在核酶、病毒接吻环、病毒内部核糖体进入位点和纳米生物学领域的应用示例。
