Comprehensive automation for NMR structure determination of proteins

Methods in Molecular Biology

Volumn 831, Issue , 2012, Pages 429-451

  Guerry, Paul ^a   Herrmann, Torsten ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

ASCAN; ATNOS; Automated NMR structure determination; CANDID; MATCH; NMR structure determination; NOE assignment; Protein structure; Resonance assignment; UNIO protocol

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTER GRAPHICS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84855878395     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-480-3_22     Document Type: Article

References (67)

1. Billeter, M., Wagner, G., and Wüthrich, K. (2008) Solution NMR structure determination of proteins revisited. J. Biomol. NMR 42, 155-158.
2. Williamson, M. P., and Craven, C. J. (2009) Automated protein structure calculation from NMR data. J. Biomol. NMR 43, 131-143.
3. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. Wiley, New York.
4. Altieri, A. S., and Byrd, R. A. (2004) Automation of NMR structure determination of proteins. Curr. Opin. Struct. Biol. 14, 547-553. (Pubitemid 39311817)
5. Baran, M. C., Huang, Y. J., Moseley, H. N. B., and Montelione, G. T. (2004) Automated analysis of protein NMR assignments and structures. Chem. Rev. 104, 3541-3555.
6. Huang, Y. P. J., Moseley, H. N. B., Baran, M. C., Arrowsmith, C., Powers, R., Tejero, R., et al. (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol. 394, 111-141. (Pubitemid 40460914)
7. Gronwald, W., and Kalbitzer, H. R. (2004) Automated structure determination of proteins by NMR spectroscopy. Prog. Nucl. Magn. Reson. Spectrosc. 44, 33-96.
8. Güntert, P. (2009) Automated structure determination from NMR spectra. Eur. Biophys. J. 38, 129-143.
9. Kraulis, P. J. (1989) Ansig - a Program for the Assignment of Protein H-1 2d-Nmr Spectra by Interactive Computer-Graphics. J. Magn. Reson. 84, 627-633.
10. Johnson, B. A., and Blevins, R. A. (1994) Nmr View - a Computer-Program for the Visualization and Analysis of Nmr Data. J. Biomol. NMR 4, 603-614.
11. Bartels, C., Xia, T. H., Billeter, M., Güntert, P., and Wüthrich, K. (1995) The Program Xeasy for Computer-Supported Nmr Spectral-Analysis of Biological Macromolecules. J. Biomol. NMR 6, 1-10.
12. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) Nmrpipe - a Multidimensional Spectral Processing System Based on Unix Pipes. J. Biomol. NMR 6, 277-293.
13. Neidig, K. P., Geyer, M., Gorler, A., Antz, C., Saffrich, R., Beneicke, W., et al. (1995) Aurelia, a Program for Computer-Aided Analysis of Multidimensional Nmr-Spectra. J. Biomol. NMR 6, 255-270.
14. Goddard, T. D., and Kneller, D. G. (2001) SPARKY 3. University of Californai, San Francisco.
15. Keller, R. L. J. (2004) Optimizing the process of nuclear magnetic resonance spectrum analysis and computer aided resonance assignment. Ph.D. thesis. Diss. ETH Nr. 15947. ETH Zurich, Zurich, Switzerland.
16. Kobayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Güntert, P., et al. (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J. Biomol. NMR 39, 31-52. (Pubitemid 47249693)
17. Mumenthaler, C., Güntert, P., Braun, W., and Wüthrich, K. (1997) Automated combined assignment of NOESY spectra and threedimensional protein structure determination. J. Biomol. NMR 10, 351-362. (Pubitemid 127505375)
18. Gronwald, W., Moussa, S., Elsner, R., Jung, A., Ganslmeier, B., Trenner, J., et al. (2002) Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J. Biomol. NMR 23, 271-287. (Pubitemid 35174616)
19. Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319, 209-227. (Pubitemid 34729497)
20. Linge, J. P., Habeck, M., Rieping, W., and Nilges, M. (2003) ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315-316. (Pubitemid 36181930)
21. Kuszewski, J., Schwieters, C. D., Garrett, D. S., Byrd, R. A., Tjandra, N., and Clore, G. M. (2004) Completely automated, highly errortolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. J. Am. Chem. Soc. 126, 6258-6273. (Pubitemid 38657053)
22. Huang, Y. J., Tejero, R., Powers, R., and Montelione, G. T. (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Methods Enzymol 62, 587-603. (Pubitemid 43191247)
23. Güntert, P. (2003) Automated NMR protein structure calculation. Prog. Nucl. Magn. Reson. Spectrosc. 43, 105-125.
24. Bernstein, R., Cieslar, C., Ross, A., Oschkinat, H., Freund, J., and Holak, T. A. (1993) Computer-Assisted Assignment of Multidimensional Nmr-Spectra of Proteins-Application to 3d Noesy-Hmqc and Tocsy-Hmqc Spectra. J. Biomol. NMR 3, 245-251.
25. Olson, J. B., and Markley, J. L. (1994) Evaluation of an Algorithm for the Automated Sequential Assignment of Protein Backbone Resonances - a Demonstration of the Connectivity Tracing Assignment Tools (Contrast) Software Package. J. Biomol. NMR 4, 385-410.
26. Lukin, J. A., Gove, A. P., Talukdar, S. N., and Ho, C. (1997) Automated probabilistic method for assigning backbone resonances of (C-13,N-15)-labeled proteins. J. Biomol. NMR 9, 151-166. (Pubitemid 127715706)
27. Bartels, C., Güntert, P., Billeter, M., and Wüthrich, K. (1997) GARANT - A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J. Comput. Chem. 18, 139-149. (Pubitemid 127599839)
28. Choy, W. Y., Sanctuary, B. C., and Zhu, G. (1997) Using neural network predicted secondary structure information in automatic protein NMR assignment. J. Chem. Inf. Comput. Sci. 37, 1086-1094. (Pubitemid 127599807)
29. Buchler, N. E. G., Zuiderweg, E. R. P., Wang, H., and Goldstein, R. A. (1997) Protein NMR assignments using mean-field simulated annealing. Biophys. J. 72, Wp447-Wp447.
30. Croft, D., Kemmink, J., Neidig, K. P., and Oschkinat, H. (1997) Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques. J. Biomol. NMR 10, 207-219. (Pubitemid 127504667)
31. Zimmerman, D. E., Kulikowski, C. A., Huang, Y. P., Feng, W. Q., Tashiro, M., Shimotakahara, S., et al. (1997) Automated analysis of protein NMR assignments using methods from artifi-cial intelligence. J. Mol. Biol. 269, 592-610. (Pubitemid 27267872)
32. Gronwald, W., Willard, L., Jellard, T., Boyko, R. E., Rajarathnam, K., Wishart, D. S., et al. (1998) CAMRA: Chemical shift based computer aided protein NMR assignments. J. Biomol. NMR 12, 395-405. (Pubitemid 128511305)
33. Leutner, M., Gschwind, R. M., Liermann, J., Schwarz, C., Gemmecker, G., and Kessler, H. (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J. Biomol. NMR 11, 31-43. (Pubitemid 128510225)
34. Moseley, H. N. B., Monleon, D., and Montelione, G. T. (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Nuc. Magn. Reson. Biol. Macromol. 339, 91-108. (Pubitemid 32666558)
35. Coggins, B. E., and Zhou, P. (2003) PACES: Protein sequential assignment by computerassisted exhaustive search. J. Biomol. NMR 26, 93-111. (Pubitemid 36609043)
36. Malmodin, D., Papavoine, C. H. M., and Billeter, M. (2003) Fully automated sequencespecific resonance assignments of heteronuclear protein spectra. J. Biomol. NMR 27, 69-79. (Pubitemid 36987111)
37. Hitchens, T. K., Lukin, J. A., Zhan, Y. P., McCallum, S. A., and Rule, G. S. (2003) MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J. Biomol. NMR 25, 1-9. (Pubitemid 36181757)
38. Moseley, H. N. B., Riaz, N., Aramini, J. M., Szyperski, T., and Montelione, G. T. (2004) A generalized approach to automated NMR peak list editing: application to reduced dimensionality triple resonance spectra. J. Magn. Reson. 170, 263-277.
39. Eghbalnia, H. R., Bahrami, A., Wang, L. Y., Assadi, A., and Markley, J. L. (2005) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO). J. Biomol. NMR 32, 219-233. (Pubitemid 41258802)
40. Lin, H. N., Wu, K. P., Chang, J. M., Sung, T. Y., and Hsu, W. L. (2005) GANA - a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res. 33, 4593-4601.
41. Masse, J. E., Keller, R., and Pervushin, K. (2006) SideLink: Automated side-chain assignment of biopolymers from NMR data by relative-hypothesis- prioritization-based simulated logic. J. Magn. Reson. 181, 45-67. (Pubitemid 43866538)
42. Masse, J. E., and Keller, R. (2005) AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relativehypothesis- prioritization-based simulated logic. J. Magn. Reson. 174, 133-151. (Pubitemid 40423617)
43. Wang, J. Y., Wang, T. Z., Zuiderweg, E. R. P., and Crippen, G. M. (2005) CASA: An efficient automated assignment of protein mainchain NMR data using an ordered tree search algorithm. J. Biomol. NMR 33, 261-279. (Pubitemid 43118578)
44. Kamisetty, H., Bailey-Kellogg, C., and Pandurangan, G. (2006) An efficient randomized algorithm for contact-based NMR backbone resonance assignment. Bioinformatics 22, 172-180. (Pubitemid 43205403)
45. Vitek, O., Bailey-Kellogg, C., Craig, B., and Vitek, J. (2006) Inferential backbone assignment for sparse data. J. Biomol. NMR 35, 187-208. (Pubitemid 44151639)
46. Wu, K. P., Chang, J. M., Chen, J. B., Chang, C. F., Wu, W. J., Huang, T. H., et al. (2006) RIBRA-An error-tolerant algorithm for the NMR backbone assignment problem. J. Comput. Biol. 13, 229-244.
47. Volk, J., Herrmann, T., and Wüthrich, K. (2008) Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J. Biomol. NMR 41, 127-138.
48. Fiorito, F., Herrmann, T., Damberger, F. F., and Wüthrich, K. (2008) Automated amino acid side-chain NMR assignment of proteins using C-13-and N-15-resolved 3D [H-1,H-1]-NOESY. J. Biomol. NMR 42, 23-33.
49. Neidig, K. P., Saffrich, R., Lorenz, M., and Kalbitzer, H. R. (1990) Cluster-Analysis and Multiplet Pattern-Recognition in 2-Dimensional Nmr-Spectra. J. Magn. Reson. 89, 543-552.
50. Garrett, D. S., Powers, R., Gronenborn, A. M., and Clore, G. M. (1991) A Common-Sense Approach to Peak Picking in 2-Dimensional, 3-Dimensional, and 4-Dimensional Spectra Using Automatic Computer-Analysis of Contour Diagrams. J. Magn. Reson. 95, 214-220.
51. Carrara, E. A., Pagliari, F., and Nicolini, C. (1993) Neural Networks for the Peak-Picking of Nuclear-Magnetic-Resonance Spectra. Neural Networks 6, 1023-1032.
52. Antz, C., Neidig, K. P., and Kalbitzer, H. R. (1995) A General Bayesian Method for an Automated Signal Class Recognition in 2d Nmr-Spectra Combined with a Multivariate Discriminant-Analysis. J. Biomol. NMR 5, 287-296.
53. Koradi, R., Billeter, M., Engeli, M., Güntert, P., and Wüthrich, K. (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J. Magn. Reson. 135, 288-297. (Pubitemid 128452124)
54. Herrmann, T., Güntert, P., and Wüthrich, K. (2002) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J. Biomol. NMR 24, 171-189. (Pubitemid 36113646)
55. Dancea, F., and Gunther, U. (2005) Automated protein NMR structure determination using wavelet de-noised NOESY spectra. J. Biomol. NMR 33, 139-152. (Pubitemid 43149364)
56. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Cryst. D 54, 905-921.
57. Schwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65-73.
58. Güntert, P., Mumenthaler, C., and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298. (Pubitemid 27460230)
59. Doreleijers, J. F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., et al. (2003) BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J. Biomol. NMR 26, 139-146. (Pubitemid 36609046)
60. Hiller, S., Wider, G., and Wüthrich, K. (2008) APSY-NMR with proteins: practical aspects and backbone assignment. J. Biomol. NMR 42, 179-195.
61. Hiller, S., Fiorito, F., Wüthrich, K., and Wider, G. (2005) Automated projection spectroscopy (APSY). Proc. Natl. Acad. Sci. USA 102, 10876-10881. (Pubitemid 41105960)
62. Güntert, P., and Wüthrich, K. (1992) Flatt - a New Procedure for High-Quality Base-Line Correction of Multidimensional Nmr-Spectra. J. Magn. Reson. 96, 403-407.
63. Nilges, M. (1995) Calculation of Protein Structures with Ambiguous Distance Restraints-Automated Assignment of Ambiguous Noe Crosspeaks and Disulfide Connectivities. J. Mol. Biol. 245, 645-660.
64. Kuszewski, J. J., Thottungal, R. A., Clore, G. M., and Schwieters, C. D. (2008) Automated errortolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm. J. Biomol. NMR 41, 221-239.
65. Schwieters, C. D., Kuszewski, J. J., and Clore, G. M. (2006) Using Xplor-NIH for NMR molecular structure determination. Prog. Nucl. Magn. Reson. Spectrosc. 48, 47-62.
66. Fiorito, F., Hiller, S., Wider, G., and Wüthrich, K. (2006) Automated resonance assignment of proteins: 6D APSY-NMR. J. Biomol. NMR 35, 27-37. (Pubitemid 43941721)
67. Nilges, M. (1993) A Calculation Strategy for the Structure Determination of Symmetrical Dimers by H-1-Nmr. Proteins 17, 297-309. (Pubitemid 23331459)