NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.
Bioinformatics. 2014 Dec 12;
Authors: Lee W, Tonelli M, Markley JL
Abstract
SUMMARY: SPARKY (Goddard & 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 (Lee et al. 2012), greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web-servers including, PECAN (Eghbalnia et al. 2005), PINE (Bahrami et al. 2009), TALOS-N (Shen and Bax 2013), CS-Rosetta (Shen et al. 2009), SHIFTX2 (Han et al. 2011) and PONDEROSA-C/S (Lee et al. 2014). Availability: 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-sp...stribution.htm.
CONTACT: whlee@nmrfam.wisc.edu; markley@nmrfam.wisc.edu.
PMID: 25505092 [PubMed - as supplied by publisher]
Postdoc NMRFAM
Postdoc NMRFAM
The National Magnetic Resonance Facility at Madison (NMRFAM) has immediate openings for two postdoctoral research associates. Please visit the NMRFAM website www.nmrfam.wisc.edu for information about our instrumentation and research programs. (1) Structure determination by hybrid methods (NMR, SAXS, computation) The ideal candidate will be a recent PhD with experience in solution structure determination making use of data from NMR spectroscopy and small angle X-ray scattering (SAXS). This position will work with NMRFAM staff members developing technology and applying it to...
nmrlearner
Job marketplace
0
08-07-2012 05:55 PM
Biomolecular structure refinement using the GROMOS simulation software
Biomolecular structure refinement using the GROMOS simulation software
Abstract For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions...
nmrlearner
Journal club
1
08-25-2011 07:03 AM
[BMNRC community] National Magnetic Resonance Facility at Madison (NMRFAM)
National Magnetic Resonance Facility at Madison (NMRFAM)
The National Magnetic Resonance Facility at Madison (NMRFAM) is a state of the art NMR spectrometer facility located in the*
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.
Linear Mode
