Lee Woonghee, Tonelli Marco, Markley John L
National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
Bioinformatics. 2015 Apr 15;31(8):1325-7. doi: 10.1093/bioinformatics/btu830. Epub 2014 Dec 12.
SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S.
The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm.
whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu
Supplementary data are available at Bioinformatics online.
尽管SPARKY(戈达德和克内勒,SPARKY 3)的原始开发者在2001年停止了该软件包的开发,但它仍然是核磁共振数据分析中最受欢迎的软件程序。我们接手了该软件包的开发,并介绍了NMRFAM-SPARKY,它实现了反映生物分子核磁共振领域进展的新功能。NMRFAM-SPARKY已与当前版本的Python和Tcl/Tk重新打包,这些版本支持用于核磁共振峰模拟和图形归属确定的新工具。这些工具,连同来自PACSY数据库的化学位移预测,极大地加速了蛋白质侧链的归属。NMRFAM-SPARKY支持自动数据格式相互转换,以便与包括PECAN、PINE、TALOS-N、CS-Rosetta、SHIFTX2和PONDEROSA-C/S在内的各种网络服务器接口。
该软件包以及二进制文件和源代码(如有需要)可从http://pine.nmrfam.wisc.edu/download_packages.html免费下载。使用手册和视频教程可在http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm找到。
whlee@nmrfam.wisc.edu或markley@nmrfam.wisc.edu
补充数据可在《生物信息学》在线获取。