PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.
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DOI：
10.1093/bioinformatics/btp345
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发表时间：
2009-08-15
期刊：
影响因子：
--
通讯作者：
Markley JL
中科院分区：
文献类型：
--
作者：
Lee W;Westler WM;Bahrami A;Eghbalnia HR;Markley JL
总结：PINE-SPARKY支持在实验核磁共振光谱背景下快速、用户友好且高效地可视化蛋白质共价结构中特定原子的核磁共振化学位移的概率分配。PINE-SPARKY基于非常流行的SPARKY软件包，用于可视化多维NMR光谱（T。D.戈达德和D. G. Kneller，SPARKY 3，加州大学，旧金山弗朗西斯科）。PINE-SPARKY由一个转换器（PINE 2SPARKY）组成，该转换器从自动化PINE-NMR分析中获取输出并将其转换为SPARKY输入，以及一些SPARKY扩展。在PINE-NMR步骤中获得的电子和它们的概率在SPARKY的光谱视图中被可视化为标签。三个SPARKY扩展（PINE Assigner、PINE Graph Assigner和Assign the Best by PINE）用于操作表示分配及其概率的标签。PINE Assigner列出对话框中选定峰的所有可能分配，并允许用户在其中进行选择。PINE Graph Assigner中的窗口显示选定残基中的所有原子沿着及其相邻残基中的所有原子;此外，它还显示任何选定原子的PINE衍生连接性分配的分级列表。指定PINE最佳值允许用户选择一个概率阈值，并自动将高于该阈值的所有指定接受为“固定”;在此操作之后，仅需要目视检查不太确定的指定。一旦分配固定，PINE-SPARKY生成的输出文件可以用作PINE-NMR的输入，以进行进一步的改进。可用性：该程序以源代码和二进制代码的形式提供，沿着教程和参考手册，可在http://pine.nmrfam.wisc.edu/PINE-SPARKY上获得。联系方式：whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu
Summary: PINE-SPARKY supports the rapid, user-friendly and efficient visualization of probabilistic assignments of NMR chemical shifts to specific atoms in the covalent structure of a protein in the context of experimental NMR spectra. PINE-SPARKY is based on the very popular SPARKY package for visualizing multidimensional NMR spectra (T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco). PINE-SPARKY consists of a converter (PINE2SPARKY), which takes the output from an automated PINE-NMR analysis and transforms it into SPARKY input, plus a number of SPARKY extensions. Assignments and their probabilities obtained in the PINE-NMR step are visualized as labels in SPARKY's spectrum view. Three SPARKY extensions (PINE Assigner, PINE Graph Assigner, and Assign the Best by PINE) serve to manipulate the labels that signify the assignments and their probabilities. PINE Assigner lists all possible assignments for a peak selected in the dialog box and enables the user to choose among these. A window in PINE Graph Assigner shows all atoms in a selected residue along with all atoms in its adjacent residues; in addition, it displays a ranked list of PINE-derived connectivity assignments to any selected atom. Assign the Best-by-PINE allows the user to choose a probability threshold and to automatically accept as “fixed” all assignments above that threshold; following this operation, only the less certain assignments need to be examined visually. Once assignments are fixed, the output files generated by PINE-SPARKY can be used as input to PINE-NMR for further refinements. Availability: The program, in the form of source code and binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/PINE-SPARKY. Contact: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu
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