FLYA
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| − | Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. | + | Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. The core FLYA algorithm determines chemical shift assignments for all <sup>1</sup>H, <sup>13</sup>C, and <sup>15</sup>N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination. |
== Availability == | == Availability == | ||
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* Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt15-AutomatedNMR.pdf .] [http://dx.doi.org/10.1007/978-1-4939-2230-7_16 Meth. Mol. Biol. 1261, 303–329 (2015)] | * Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Schmidt15-AutomatedNMR.pdf .] [http://dx.doi.org/10.1007/978-1-4939-2230-7_16 Meth. Mol. Biol. 1261, 303–329 (2015)] | ||
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| + | Combined automated NOESY cross peak assignment and structure calculation: | ||
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| + | * Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)] | ||
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| + | Evaluation of combined automated NOESY cross peak assignment and structure calculation | ||
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| + | * Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Buchner15-NoeassignEvaluation.pdf .] [http://dx.doi.org/10.1007/s10858-015-9921-z J. Biomol. NMR 62, 81–95 (2015)] | ||
Revision as of 17:07, 16 November 2015
Fully automated structure determination of proteins in solution
Fully automated structure determination of proteins in solution (FLYA) yields, without human intervention, three-dimensional protein structures starting from a set of multidimensional NMR spectra. The core FLYA algorithm determines chemical shift assignments for all 1H, 13C, and 15N nuclei, the assignment of NOESY cross-peaks, the generation of distance restraints, and the calculation of the three-dimensional structure by torsion angle dynamics. The resulting, preliminary structure serves as additional input to the second stage of the procedure, in which a new ensemble of chemical shift assignments and a refined structure are calculated. The purely computational FLYA method is suitable for substituting all manual spectra analysis and thus overcomes a main efficiency limitation of the NMR method for protein structure determination.
Availability
- FLYA calculations are carried out with the program CYANA. FLYA is not available as a separate program.
References
FLYA algorithm:
- Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment. J. Am. Chem. Soc. 134, 12817–12829 (2012)
FLYA applications:
- Schmidt, E., Gath, J., Habenstein, B., Ravotti, F., Székely, K., Huber, M., Buchner, L., Böckmann, A., Meier, B. H. & Güntert, P. Automated solid-state NMR resonance assignment of protein microcrystals and amyloids. J. Biomol. NMR 56, 243–254 (2013)
- Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. J. Biomol. NMR 57, 193-204 (2013)
- Aeschbacher, T., Schmidt, E., Blatter, M., Maris, C., Duss, O., Allain, F. H.-T., Güntert, P. & Schubert, M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucl. Acids Res. 41, e172 (2013)
- Krähenbühl, B., El Bakkali, I., Schmidt, E., Güntert, P. & Wider, G. Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments. J. Biomol. NMR 59, 87-93 (2014)
- Schmidt, E., Ikeya, T., Takeda, M., Löhr, F., Buchner, L., Ito, Y., Kainosho, M. & Güntert, P. Automated resonance assignment of the 21 kDa stereo-array isotope labeled thioldisulfide oxidoreductase DsbA. J. Magn. Reson. 249, 88–93 (2014)
- Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra. Meth. Mol. Biol. 1261, 303–329 (2015)
Combined automated NOESY cross peak assignment and structure calculation:
- Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453-471 (2015)
Evaluation of combined automated NOESY cross peak assignment and structure calculation
- Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 81–95 (2015)
