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Bioinformatics Advance Access originally published online on June 3, 2009
Bioinformatics 2009 25(16):2085-2087; doi:10.1093/bioinformatics/btp345
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy

Woonghee Lee 1,*, William M. Westler 1, Arash Bahrami 1, Hamid R. Eghbalnia 2 and John L. Markley 1,*

1 National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706 and 2 Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA

*To whom correspondence should be addressed.


  Abstract

Summary: PINE-SPARKY supports the rapid, user-friendly and efficient visualization of probabilistic assignments of NMR chemical shifts to specific atoms in the covalent structure of a protein in the context of experimental NMR spectra. PINE-SPARKY is based on the very popular SPARKY package for visualizing multidimensional NMR spectra (T. D. Goddard and D. G. Kneller, SPARKY 3, University of California, San Francisco). PINE-SPARKY consists of a converter (PINE2SPARKY), which takes the output from an automated PINE-NMR analysis and transforms it into SPARKY input, plus a number of SPARKY extensions. Assignments and their probabilities obtained in the PINE-NMR step are visualized as labels in SPARKY's spectrum view. Three SPARKY extensions (PINE Assigner, PINE Graph Assigner, and Assign the Best by PINE) serve to manipulate the labels that signify the assignments and their probabilities. PINE Assigner lists all possible assignments for a peak selected in the dialog box and enables the user to choose among these. A window in PINE Graph Assigner shows all atoms in a selected residue along with all atoms in its adjacent residues; in addition, it displays a ranked list of PINE-derived connectivity assignments to any selected atom. Assign the Best-by-PINE allows the user to choose a probability threshold and to automatically accept as "fixed" all assignments above that threshold; following this operation, only the less certain assignments need to be examined visually. Once assignments are fixed, the output files generated by PINE-SPARKY can be used as input to PINE-NMR for further refinements.

Availability: The program, in the form of source code and binary code along with tutorials and reference manuals, is available at http://pine.nmrfam.wisc.edu/PINE-SPARKY.

Contact: whlee{at}nmrfam.wisc.edu; markley{at}nmrfam.wisc.edu

Associate Editor: Burkhard Rost

Received on April 10, 2009; revised on May 29, 2009; accepted on May 29, 2009

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