Advertisement

XIPP: multi-dimensional NMR analysis software

  • Daniel S. GarrettEmail author
  • Mengli Cai
  • G. Marius CloreEmail author
Article

Abstract

Here we present the XIPP (eXtensible Interactive Peak Picker) NMR software for analyzing multidimensional NMR data of proteins, DNA, RNA and protein-nucleic acid complexes. XIPP organizes experiments into pre-defined studies and replaces our original PIPP software suite which is no longer supported. Default study types exist for backbone assignment, sidechain assignment, NOE assignment and several relaxation series experiments, used in solution NMR studies. XIPP is written in Java and Jython. The default study types are defined in Jython which can be modified and extended to create new types of studies.

Keywords

Multidimensional NMR Spectral assignment Spectral analysis 

Notes

Acknowledgements

This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (to G.M.C.)

Funding

This study was funded by NIDDK (Grant No. DK-029023).

References

  1. Anthis NJ, Clore GM (2015) Visualizing transient dark states by NMR spectroscopy. Q Rev Biophys 48:35–116CrossRefGoogle Scholar
  2. Bartels C, Xia TH, Billeter M, Guntert P, Wuthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10CrossRefGoogle Scholar
  3. Bax A, Grzesiek S (1993) Methodological advances in protein NMR. Acc Chem Res 26:131–138CrossRefGoogle Scholar
  4. Beazley DM (2009) Python essential reference. Addison-Wesley, Upper Saddle RiverGoogle Scholar
  5. Clore GM, Gronenborn AM (1991) Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science 252:1390–1399ADSCrossRefGoogle Scholar
  6. Clore GM, Gronenborn AM (1998) Determining the structures of large proteins and protein complexes by NMR. Trends Biotechnol 16:22–34CrossRefGoogle Scholar
  7. Clore GM, Kay LE, Bax A, Gronenborn AM (1991) Four-dimensional 13C/13C-edited nuclear Overhauser enhancement spectroscopy of a protein in solution—application to interleukin-1β. Biochemistry 30:12–18CrossRefGoogle Scholar
  8. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J et al (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  9. Eccles C, Guntert P, Billeter M, Wuthrich K (1991) Efficient analysis of protein 2D NMR spectra using the software package EASY. J Biomol NMR 1:111–130CrossRefGoogle Scholar
  10. Flanagan D (2005) Java in a nutshell. O’Reilly, BeijingzbMATHGoogle Scholar
  11. Garrett DS, Powers R, Gronenborn AM, Clore GM (1991) A common-sense approach to peak picking in two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J Magn Reson 95:214–220ADSGoogle Scholar
  12. Garrett D, Seok Y, Peterkofsky A, Clore G, Gronenborn A (1997) Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N-terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry 36:4393–4398CrossRefGoogle Scholar
  13. Garrett D, Seok Y, Peterkofsky A, Gronenborn A, Clore G (1999) Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr. Nat Struct Biol 6:166–173CrossRefGoogle Scholar
  14. Harold ER, Means WS (2004) XML in a nutshell. O’Reilly, BeijingzbMATHGoogle Scholar
  15. Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352Google Scholar
  16. Johnson BA, Blevins RA (1994) NMRView - a computer-program for the visualization and analysis of nmr data. J Biomol NMR 4:603–614CrossRefGoogle Scholar
  17. Jung Y, Zweckstetter M (2004) Mars—robust automatic backbone assignment of proteins. J Biomol NMR 30:11–23CrossRefGoogle Scholar
  18. Kay LE, Clore GM, Bax A, Gronenborn AM (1990) Four-dimensional heteronuclear triple resonance NMR spectroscopy of interleukin-1β in solution. Science 249:411–414ADSCrossRefGoogle Scholar
  19. Keller RLJ (2004) The computer aided resonance tutorial. CANTINA Verlag, GoldauGoogle Scholar
  20. Kraulis PJ (1989) Ansig—a program for the sssignment of protein 1H 2D NMR spectra by interactive computer graphics. J Magn Reson 84:627–633ADSGoogle Scholar
  21. Kraulis PJ, Domaille PJ, Campbell-Burk SL, Van Aken T, Laue ED (1994) Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry 33:3515–3531CrossRefGoogle Scholar
  22. Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327CrossRefGoogle Scholar
  23. Libich DS, Tugarinov V, Clore GM (2015) Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR. Proc Natl Acad Sci USA 112:8817–8823ADSCrossRefGoogle Scholar
  24. Narayanan R, Durr U, Bibow S, Biernat J, Mandelkow E et al (2010) Automatic assignment of the intrinsically disordered protein tau with 441-residues. J Am Chem Soc 132:11906–11907CrossRefGoogle Scholar
  25. Pedroni S, Rappin N (2002) Jython essentials. O’Reilly, BeijingGoogle Scholar
  26. Schwieters CD, Kuszewski JJ, Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Progr Nucl Magn Reson Spectr 48:47–62CrossRefGoogle Scholar
  27. Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG et al (2016) CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. J Biomol NMR 66:111–124CrossRefGoogle Scholar
  28. Tugarinov V, Libich DS, Meyer V, Roche J, Clore GM (2015) The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy. Angew Chem Int Ed Engl 54:11157–11161CrossRefGoogle Scholar
  29. Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696CrossRefGoogle Scholar
  30. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New YorkCrossRefGoogle Scholar

Copyright information

© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2019

Authors and Affiliations

  1. 1.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaUSA

Personalised recommendations