NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
By Woonghee Lee, Marco Tonelli, John L. Markley. 2014
1,872 citations recorded by the source corpus.
Summary: 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. Availability and implementation: 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. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- David Baker
- Sergey Ovchinnikov
- Frank DiMaio
- Woonghee Lee
- John L. Markley
- Ivan V. Anishchenko
- Gaetano T. Montelione
- Marco Tonelli
In Molecular Biology
- David Baker
- Sergey Ovchinnikov
- Frank DiMaio
- Ivan V. Anishchenko
- Woonghee Lee
- John L. Markley
- Tanja Kortemme
- Daniel‐Adriano Silva
Citations in the corpus
- De novo protein design by deep network hallucination (2020, methodology): “All NMR spectra were processed using NMRPipe and NMRDraw 38 and visualized in NMRFAM-SPARKY 39 .”
- Integrative NMR for biomolecular research (2016, positive): “Tasks are conducted by enhanced versions of two main software packages, NMRFAM-SPARKY (Lee et al. 2015) and PONDEROSA (Lee et al.”
- The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data (2016, methodology): “We have been developing an integrated approach to NMR-based protein structure determination that builds on NMRFAM - SPARKY (Lee et al. 2015), an updated and extended version of the highly popular Sparky program (Goddard and Kneller 2008).”
- De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures (2017, methodology): “Spectra were analyzed with XEASY(18) and visualized by Sparky.(19) Distance restrains derived from cross-peak intensities in NOESY spectra were used for the structural calculation of 2H and 2H-4.”
- NMRbox: A Resource for Biomolecular NMR Computation. (2017, methodology): “These build on the existing CONNJUR-WB system (22) and extensions to NMRFAM-SPARKY (10,23) for annotating manual edits to peak lists.”