NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

December 8, 2014 | Woonghee Lee, Marco Tonelli and John L. Markley
NMRFAM-SPARKY is an enhanced version of the SPARKY software, which remains the most popular tool for NMR data analysis. Developed by the authors, NMRFAM-SPARKY incorporates new functions reflecting advances in biomolecular NMR. It uses updated versions of Python and Tcl/Tk, supporting new tools for NMR peak simulation and graphical assignment. These tools, along with chemical shift predictions from the PACSY database, accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format conversion for interfacing with web servers such as PECAN, PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. The software is available for free download from http://pine.nmrfam.wisc.edu/download_packages.html. It includes instruction manuals and video tutorials at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. NMRFAM-SPARKY includes new functions such as Dummy Graph and Transfer and Simulate Assignments. The Dummy Graph provides a graphical interface for real-time visualization of sequence information and assignment situations. The Transfer and Simulate Assignments function uses statistics from the PACSY database to simulate resonance frequencies based on various conditions. This tool enables a new predict-and-confirm approach to resonance assignments, which is faster than the traditional pick-and-assign method. NMRFAM-SPARKY also includes structure prediction tools such as PECAN, TALOS-N and CS-Rosetta. These tools can be used to predict the 3D structure so that side chain and NOE assignments can be refined through combined use of CS-Rosetta and SHIFTX2. The software also contains updated chemical shift statistics, which improve the accuracy and reliability of predictions. The number of resonance types was expanded from 273 to 276, and the statistical significance of 27 of these resonance types was improved. NMRFAM-SPARKY has been downloaded 155 times since its release. The authors expect that its use will increase the success rate of automated assignment runs on the PINE server and automated structure determinations on the PONDEROSA-C/S server. The software is expected to improve the reliability and successful use of other programs or web servers such as TALOS-N and CS-Rosetta.NMRFAM-SPARKY is an enhanced version of the SPARKY software, which remains the most popular tool for NMR data analysis. Developed by the authors, NMRFAM-SPARKY incorporates new functions reflecting advances in biomolecular NMR. It uses updated versions of Python and Tcl/Tk, supporting new tools for NMR peak simulation and graphical assignment. These tools, along with chemical shift predictions from the PACSY database, accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format conversion for interfacing with web servers such as PECAN, PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. The software is available for free download from http://pine.nmrfam.wisc.edu/download_packages.html. It includes instruction manuals and video tutorials at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. NMRFAM-SPARKY includes new functions such as Dummy Graph and Transfer and Simulate Assignments. The Dummy Graph provides a graphical interface for real-time visualization of sequence information and assignment situations. The Transfer and Simulate Assignments function uses statistics from the PACSY database to simulate resonance frequencies based on various conditions. This tool enables a new predict-and-confirm approach to resonance assignments, which is faster than the traditional pick-and-assign method. NMRFAM-SPARKY also includes structure prediction tools such as PECAN, TALOS-N and CS-Rosetta. These tools can be used to predict the 3D structure so that side chain and NOE assignments can be refined through combined use of CS-Rosetta and SHIFTX2. The software also contains updated chemical shift statistics, which improve the accuracy and reliability of predictions. The number of resonance types was expanded from 273 to 276, and the statistical significance of 27 of these resonance types was improved. NMRFAM-SPARKY has been downloaded 155 times since its release. The authors expect that its use will increase the success rate of automated assignment runs on the PINE server and automated structure determinations on the PONDEROSA-C/S server. The software is expected to improve the reliability and successful use of other programs or web servers such as TALOS-N and CS-Rosetta.
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