Automated Structure Determination from NMR Spectra

  • Sina Kazemi
  • Julia Maren Würz
  • Elena Schmidt
  • Anurag Bagaria
  • Peter GüntertEmail author
Reference work entry


The steps of an NMR protein structure determination that follow data acquisition can now be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis highlights recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package.


Peak picking Resonance assignment NOE assignment Structure calculation FLYA CYANA 


  1. 1.
    Billeter M, Wagner G, Wüthrich K. Solution NMR structure determination of proteins revisited. J Biomol NMR. 2008;42:155–8.CrossRefGoogle Scholar
  2. 2.
    Gronwald W, Kalbitzer HR. Automated structure determination of proteins by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc. 2004;44:33–96.CrossRefGoogle Scholar
  3. 3.
    Güntert P. Automated NMR protein structure calculation. Prog Nucl Magn Reson Spectrosc. 2003;43:105–25.CrossRefGoogle Scholar
  4. 4.
    Malmodin D, Billeter M. High-throughput analysis of protein NMR spectra. Prog Nucl Magn Reson Spectrosc. 2005;46:109–29.CrossRefGoogle Scholar
  5. 5.
    Kainosho M, Güntert P. SAIL – Stereo-array isotope labeling. Q Rev Biophys. 2009;42:247–300.CrossRefGoogle Scholar
  6. 6.
    Schmidt E, Güntert P. A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc. 2012;134:12817–29.CrossRefGoogle Scholar
  7. 7.
    Güntert P, Buchner L. Combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR. 2015;62:453–71.CrossRefGoogle Scholar
  8. 8.
    Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002;319:209–27.CrossRefGoogle Scholar
  9. 9.
    Jee J, Güntert P. Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J Struct Funct Genom. 2003;4:179–89.CrossRefGoogle Scholar
  10. 10.
    Buchner L, Güntert P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR. 2015;62:81–95.CrossRefGoogle Scholar
  11. 11.
    Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K. The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR. 1995;6:1–10.CrossRefGoogle Scholar
  12. 12.
    Goddard TD, Kneller DG. Sparky 3. San Francisco: University of California; 2001.Google Scholar
  13. 13.
    Johnson BA. Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol. 2004;278:313–52.Google Scholar
  14. 14.
    Johnson BA, Blevins RA. NMR View – a computer program for the visualization and analysis of NMR data. J Biomol NMR. 1994;4:603–14.CrossRefGoogle Scholar
  15. 15.
    Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins. 2005;59:687–96.CrossRefGoogle Scholar
  16. 16.
    Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, Vuister GW. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. J Biomol NMR. 2016;66(2):111–24.CrossRefGoogle Scholar
  17. 17.
    Liu Z, Abbas A, Jing BY, Gao X. WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering. Bioinformatics. 2012;28:914–20.CrossRefGoogle Scholar
  18. 18.
    Alipanahi B, Gao X, Karakoc E, Donaldson L, Li M. PICKY: a novel SVD-based NMR spectra peak picking method. Bioinformatics. 2009;25:i268–i75.CrossRefGoogle Scholar
  19. 19.
    Klukowski P, Walczak MJ, Gonczarek A, Boudet J, Wider G. Computer vision-based automated peak picking applied to protein NMR spectra. Bioinformatics. 2015;31:2981–8.CrossRefGoogle Scholar
  20. 20.
    Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K. Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J Magn Reson. 1998;135:288–97.CrossRefGoogle Scholar
  21. 21.
    Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR. 2002;24:171–89.CrossRefGoogle Scholar
  22. 22.
    Orekhov VY, Ibraghimov IV, Billeter M. MUNIN: a new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR. 2001;20:49–60.CrossRefGoogle Scholar
  23. 23.
    Hiller S, Fiorito F, Wüthrich K, Wider G. Automated projection spectroscopy (APSY). Proc Natl Acad Sci U S A. 2005;102:10876–81.CrossRefGoogle Scholar
  24. 24.
    Garrett DS, Powers R, Gronenborn AM, Clore GM. A common sense approach to peak picking two-, three- and four-dimensional spectra using automatic computer analysis of contour diagrams. J Magn Reson. 1991;95:214–20.Google Scholar
  25. 25.
    Würz JM, Güntert P. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK. J Biomol NMR. 2017;67:63–76.CrossRefGoogle Scholar
  26. 26.
    Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol. 1997;273:283–98.CrossRefGoogle Scholar
  27. 27.
    Cavanagh J, Fairbrother WJ, Palmer III AG, Skelton NJ, Rance M. Protein NMR spectroscopy. Principles and practice. 2nd ed. San Diego: Academic; 2007.Google Scholar
  28. 28.
    Buchner L, Schmidt E, Güntert P. Peakmatch: a simple and robust method for peak list matching. J Biomol NMR. 2013;55:267–77.CrossRefGoogle Scholar
  29. 29.
    Wüthrich K, Wider G, Wagner G, Braun W. Sequential resonance assignments as a basis for determination of spatial protein structures by high-resolution proton nuclear magnetic resonance. J Mol Biol. 1982;155:311–9.CrossRefGoogle Scholar
  30. 30.
    Guerry P, Herrmann T. Advances in automated NMR protein structure determination. Q Rev Biophys. 2011;44:257–309.CrossRefGoogle Scholar
  31. 31.
    Moseley HNB, Montelione GT. Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol. 1999;9:635–42.CrossRefGoogle Scholar
  32. 32.
    Bartels C, Güntert P, Billeter M, Wüthrich K. GARANT - A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem. 1997;18:139–49.CrossRefGoogle Scholar
  33. 33.
    Bartels C, Billeter M, Güntert P, Wüthrich K. Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR. 1996;7:207–13.CrossRefGoogle Scholar
  34. 34.
    Bahrami A, Assadi AH, Markley JL, Eghbalnia HR. Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comp Biol. 2009;5:e1000307.CrossRefGoogle Scholar
  35. 35.
    Schmucki R, Yokoyama S, Güntert P. Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm. J Biomol NMR. 2009;43:97–109.CrossRefGoogle Scholar
  36. 36.
    Zimmerman DE, Kulikowski CA, Huang YP, Feng WQ, Tashiro M, Shimotakahara S, et al. Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 1997;269:592–610.CrossRefGoogle Scholar
  37. 37.
    Güntert P, Salzmann M, Braun D, Wüthrich K. Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR. 2000;18:129–37.CrossRefGoogle Scholar
  38. 38.
    Volk J, Herrmann T, Wüthrich K. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR. 2008;41:127–38.CrossRefGoogle Scholar
  39. 39.
    Jung YS, Zweckstetter M. Mars – robust automatic backbone assignment of proteins. J Biomol NMR. 2004;30:11–23.CrossRefGoogle Scholar
  40. 40.
    Güntert P. Automated structure determination from NMR spectra. Eur Biophys J. 2009;38:129–43.CrossRefGoogle Scholar
  41. 41.
    Schmidt E, Güntert P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. J Biomol NMR. 2013;57:193–204.CrossRefGoogle Scholar
  42. 42.
    Schmidt E, Gath J, Habenstein B, Ravotti F, Székely K, Huber M, et al. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J Biomol NMR. 2013;56:243–54.CrossRefGoogle Scholar
  43. 43.
    Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, et al. BioMagResBank. Nucleic Acids Res. 2008;36:D402–D8.CrossRefGoogle Scholar
  44. 44.
    Aeschbacher T, Schmidt E, Blatter M, Maris C, Duss O, Allain FH-T, et al. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucleic Acids Res. 2013;41:e172.CrossRefGoogle Scholar
  45. 45.
    Malmodin D, Papavoine CHM, Billeter M. Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR. 2003;27:69–79.CrossRefGoogle Scholar
  46. 46.
    López-Méndez B, Güntert P. Automated protein structure determination from NMR spectra. J Am Chem Soc. 2006;128:13112–22.CrossRefGoogle Scholar
  47. 47.
    Vögeli B, Kazemi S, Güntert P, Riek R. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs. Nat Struct Mol Biol. 2012;19:1053–7.CrossRefGoogle Scholar
  48. 48.
    Güntert P, Berndt KD, Wüthrich K. The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J Biomol NMR. 1993;3:601–6.CrossRefGoogle Scholar
  49. 49.
    Skinner SP, Goult BT, Fogh RH, Boucher W, Stevens TJ, Laue ED, et al. Structure calculation, refinement and validation using CcpNmr analysis. Acta Crystallogr D. 2015;71:154–61.CrossRefGoogle Scholar
  50. 50.
    Kobayashi N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Güntert P, et al. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR. 2007;39:31–52.CrossRefGoogle Scholar
  51. 51.
    Mumenthaler C, Braun W. Automated assignment of simulated and experimental NOESY spectra of proteins by feedback filtering and self-correcting distance geometry. J Mol Biol. 1995;254:465–80.CrossRefGoogle Scholar
  52. 52.
    Mumenthaler C, Güntert P, Braun W, Wüthrich K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR. 1997;10:351–62.CrossRefGoogle Scholar
  53. 53.
    Nilges M, Macias MJ, ODonoghue SI, Oschkinat H. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol. 1997;269:408–22.CrossRefGoogle Scholar
  54. 54.
    Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M. ARIA2: Automated NOE assignment and data integration in NMR structure calculation. Bioinformatics. 2007;23:381–2.CrossRefGoogle Scholar
  55. 55.
    Huang YJ, Tejero R, Powers R, Montelione GT. A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins. 2006;62:587–603.CrossRefGoogle Scholar
  56. 56.
    Zhang Z, Porter J, Tripsianes K, Lange OF. Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta. J Biomol NMR. 2014;59:135–45.CrossRefGoogle Scholar
  57. 57.
    Nilges M. Calculation of protein structures with ambiguous distance restraints – automated assignment of ambiguous NOE crosspeaks and disulfide connectivities. J Mol Biol. 1995;245:645–60.CrossRefGoogle Scholar
  58. 58.
    Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, et al. CASD-NMR: critical assessment of automated structure determination by NMR. Nat Methods. 2009;6:625–6.CrossRefGoogle Scholar
  59. 59.
    Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, et al. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure. 2012;20:227–36.CrossRefGoogle Scholar
  60. 60.
    Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, et al. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. J Biomol NMR. 2015;62:413–24.CrossRefGoogle Scholar
  61. 61.
    Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comp Biol. 2006;2:71–9.CrossRefGoogle Scholar
  62. 62.
    Buchner L, Güntert P. Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles. Structure. 2015;23:425–34.CrossRefGoogle Scholar
  63. 63.
    López-Méndez B, Pantoja-Uceda D, Tomizawa T, Koshiba S, Kigawa T, Shirouzu M, et al. NMR assignment of the hypothetical ENTH-VHS domain At3g16270 from Arabidopsis thaliana. J Biomol NMR. 2004;29:205–6.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Sina Kazemi
    • 1
    • 2
  • Julia Maren Würz
    • 1
  • Elena Schmidt
    • 1
  • Anurag Bagaria
    • 1
  • Peter Güntert
    • 1
    • 3
    • 4
    Email author
  1. 1.Institute of Biophysical Chemistry, Center for Biomolecular Magnetic ResonanceGoethe University Frankfurt am MainFrankfurt am MainGermany
  2. 2.Frankfurt Institute for Advanced StudiesGoethe University Frankfurt am MainFrankfurt am MainGermany
  3. 3.Laboratory of Physical ChemistryETH ZürichZürichSwitzerland
  4. 4.Department of Chemistry, Graduate School of Science and EngineeringTokyo Metropolitan UniversityTokyoJapan

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