NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

12 December 2014 | Woonghee Lee*, Marco Tonelli and John L. Markley*
NMRFAM-SPARKY is an enhanced version of the popular NMR data analysis software SPARKY, developed by Woonghee Lee, Marco Tonelli, and John L. Markley. Despite SPARKY's development ceasing in 2001, NMRFAM-SPARKY introduces new features and functionalities that reflect advancements in biomolecular NMR. The software has been updated to use Python 2.7 and Tcl/Tk 8.6, enabling better compatibility with various platforms and web services. Key new features include: 1. **NMR Peak Simulation and Graphical Assignment Determination**: Tools like the Dummy Graph and Transfer and Simulate Assignments (ta) help in visualizing and verifying assignments, significantly improving the efficiency of protein side chain assignments. 2. **Automated Data Format Interconversion**: NMRFAM-SPARKY supports automated conversion between different data formats, facilitating integration with web servers such as PECAN, PINE, TALOS-N, CS-Rosetta, SHIFTX2, and PONDEROSA-C/S. 3. **Chemical Shift Predictions**: Utilizing the PACSY database, NMRFAM-SPARKY provides dynamic resonance frequency predictions based on various conditions, enhancing the accuracy and reliability of chemical shift assignments. 4. **Structure Predictions**: The software includes tools like PECAN, TALOS-N, and CS-Rosetta for predicting 3D structures, which can be used to refine side chain and NOE assignments. The availability of NMRFAM-SPARKY has been well-received, with 155 downloads over a period of several months. The authors expect that these enhancements will improve the success rate of automated assignment runs and structure determinations on various web servers.NMRFAM-SPARKY is an enhanced version of the popular NMR data analysis software SPARKY, developed by Woonghee Lee, Marco Tonelli, and John L. Markley. Despite SPARKY's development ceasing in 2001, NMRFAM-SPARKY introduces new features and functionalities that reflect advancements in biomolecular NMR. The software has been updated to use Python 2.7 and Tcl/Tk 8.6, enabling better compatibility with various platforms and web services. Key new features include: 1. **NMR Peak Simulation and Graphical Assignment Determination**: Tools like the Dummy Graph and Transfer and Simulate Assignments (ta) help in visualizing and verifying assignments, significantly improving the efficiency of protein side chain assignments. 2. **Automated Data Format Interconversion**: NMRFAM-SPARKY supports automated conversion between different data formats, facilitating integration with web servers such as PECAN, PINE, TALOS-N, CS-Rosetta, SHIFTX2, and PONDEROSA-C/S. 3. **Chemical Shift Predictions**: Utilizing the PACSY database, NMRFAM-SPARKY provides dynamic resonance frequency predictions based on various conditions, enhancing the accuracy and reliability of chemical shift assignments. 4. **Structure Predictions**: The software includes tools like PECAN, TALOS-N, and CS-Rosetta for predicting 3D structures, which can be used to refine side chain and NOE assignments. The availability of NMRFAM-SPARKY has been well-received, with 155 downloads over a period of several months. The authors expect that these enhancements will improve the success rate of automated assignment runs and structure determinations on various web servers.
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