SPARKY NMR SPECTRUM ASSIGNMENT SOFTWARE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We have developed a program called Sparky (www.cgl.ucsf.edu/home/sparky) for assignment of nuclear magnetic resonance (NMR) spectra that is widely used (a few thousand users worldwide) to determine atomic resolution structures of proteins, dna and rna in solution. About 14 percent of the 49,000 structures in the Protein Databank were solved by NMR. The basis of the technique is to identify thousands of spectral peaks that reveal distances between pairs of atoms in the molecule being studied. Those distances are used to deduce a consistent 3-dimensional shape of the molecule. A large part of the analysis involves identifying the spectral peaks, that is, determining what atoms they are associated with. This process is still largely done interactively by an NMR spectroscopist. A few programs are used for interactive peak assignment, the most popular being Sparky and NMRView. Sparky was developed in 1990 by Don Kneller working in Tack Kuntz's lab and in 1996 was taken over by Tom James' NMR lab and Tom Ferrin's Computer Graphics Lab at UC San Francisco. Many new features were developed and the program was widely distributed in the period 1996 - 2001. From 2001 to 2007 we have provided email support and maintenance but have not been adding new features to the program. The program is more widely used than ever.