FLYA - Revision history

GuentertWiki: Text replacement - "www.bpc.uni-frankfurt.de/guentert" to "uni-frankfurt.guentert.science"

2025-12-17T17:13:40Z

Text replacement - "www.bpc.uni-frankfurt.de/guentert" to "uni-frankfurt.guentert.science"

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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)]		* 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)]

			* 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[http://www.bpc.uni-frankfurt.de/guentert/Reprints/Herrmann02a.pdf .] [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]

	Evaluation of combined automated NOESY cross peak assignment and structure calculation:		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[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)]		* 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)]

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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 automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of		The core FLYA automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of
	peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins.		peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins.

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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. 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.		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 automated resonance assignment algorithm determines NMR chemical shift assignments on the basis of
			peak lists from any combination of multidimensional through-bond or through-space NMR experiments for proteins.
			Backbone and side-chain assignments can be determined. All experimental data are used simultaneously, thereby
			exploiting optimally the redundancy present in the input peak lists and circumventing potential pitfalls of
			assignment strategies in which results obtained in a given step remain fixed input data for subsequent steps.
			Instead of prescribing a specific assignment strategy, the FLYA resonance assignment algorithm requires only experimental peak lists and the primary structure of the protein, from which the peaks expected in a given
			spectrum can be generated by applying a set of rules, defined in a straightforward way by specifying through-bond
			or through-space magnetization transfer pathways. The algorithm determines the resonance assignment by finding an
			optimal mapping between the set of expected peaks that are assigned by definition but have unknown positions and
			the set of measured peaks in the input peak lists that are initially unassigned but have a known position in the spectrum. The FLYA resonance assignment algorithm thus has the reliability and flexibility to replace most manual
			and semi-automatic assignment procedures for NMR studies of proteins. Automated chemical shift assignment can be followed by combined automated NOESY assignment and structure calculation. 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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	* 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)]		* 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)]

	Evaluation of combined automated NOESY cross peak assignment and structure calculation		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[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)]		* 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)]

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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. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus 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.		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)]

			Combined automated NOESY cross peak assignment and structure calculation:

			* 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)]

			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[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)]

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 == Availability ==
-*FLYA calculations are carried out with the program [http://www.cyana.org/wiki CYANA], using the independent programs [http://www.onemoonscientific.com/ NMRView] or [[AUTOPSY]], [[GARANT]], and [[OPALp]] as additional plug-ins. FLYA is not available as a separate program.
+*FLYA calculations are carried out with the program [http://www.cyana.org/wiki CYANA]. FLYA is not available as a separate program.
 == References ==
-* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Intranet/Reprints/Lopez06a.pdf .] [http://dx.doi.org/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112–13122 (2006)]
+FLYA algorithm:

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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. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus 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.		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. Integrating existing and new software, automated peak picking over all spectra is followed by peak list filtering, the generation of an ensemble of initial chemical shift assignments, the determination of consensus 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 ==

imported>Guentert: /* References */

2009-08-14T16:11:50Z

References

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	== References ==		== References ==

	* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://dx.doi.org/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112–13122 (2006)]		* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra[http://www.bpc.uni-frankfurt.de/guentert/Intranet/Reprints/Lopez06a.pdf .] [http://dx.doi.org/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112–13122 (2006)]

imported>Masayo: /* References */

2009-06-15T14:32:08Z

References

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	== References ==		== References ==

	* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://~~pubs~~.~~acs~~.org~~/doi/abs~~/10.1021/ja061136l J. Am. Chem. Soc. 128, ~~13112-13122~~ (2006)]		* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://dx.doi.org/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112–13122 (2006)]

imported>Masayo: /* References */

2009-06-04T09:26:49Z

References

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	== References ==		== References ==

	* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://pubs.acs.org/doi/abs/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112-13122 (2006)]		* López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. [http://pubs.acs.org/doi/abs/10.1021/ja061136l J. Am. Chem. Soc. 128, 13112-13122 (2006)]
	~~:Reports or publications of results obtained with FLYA must acknowledge its use by citing this paper.~~

← Older revision		Revision as of 17:13, 17 December 2025
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	FLYA algorithm:		FLYA algorithm:

	* Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Schmidt12-AssignmentAlgorithm.pdf .] [http://dx.doi.org/10.1021/ja305091n J. Am. Chem. Soc. 134, 12817–12829 (2012)]		* Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment[http://uni-frankfurt.guentert.science/Reprints/Schmidt12-AssignmentAlgorithm.pdf .] [http://dx.doi.org/10.1021/ja305091n J. Am. Chem. Soc. 134, 12817–12829 (2012)]

	FLYA applications:		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[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Schmidt13-SolidStateFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9742-x J. Biomol. NMR 56, 243–254 (2013)]		* 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[http://uni-frankfurt.guentert.science/Reprints/Schmidt13-SolidStateFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9742-x J. Biomol. NMR 56, 243–254 (2013)]

	* Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Schmidt13-NOESYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9779-x J. Biomol. NMR 57, 193-204 (2013)]		* Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins[http://uni-frankfurt.guentert.science/Reprints/Schmidt13-NOESYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-013-9779-x 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[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Aeschbacher13-RNAFLYA.pdf .] [http://dx.doi.org/10.1093/nar/gkt665 Nucl. Acids Res. 41, e172 (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[http://uni-frankfurt.guentert.science/Reprints/Aeschbacher13-RNAFLYA.pdf .] [http://dx.doi.org/10.1093/nar/gkt665 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[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Kraehenbuehl14-APSYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-014-9829-z J. Biomol. NMR 59, 87-93 (2014)]		* 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[http://uni-frankfurt.guentert.science/Reprints/Kraehenbuehl14-APSYFLYA.pdf .] [http://dx.doi.org/10.1007/s10858-014-9829-z 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[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Schmidt14-SAILDsbA.pdf .] [http://dx.doi.org/10.1016/j.jmr.2014.10.005 J. Magn. Reson. 249, 88–93 (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[http://uni-frankfurt.guentert.science/Reprints/Schmidt14-SAILDsbA.pdf .] [http://dx.doi.org/10.1016/j.jmr.2014.10.005 J. Magn. Reson. 249, 88–93 (2014)]

	* 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://uni-frankfurt.guentert.science/Reprints/Schmidt15-AutomatedNMR.pdf .] [http://dx.doi.org/10.1007/978-1-4939-2230-7_16 Meth. Mol. Biol. 1261, 303–329 (2015)]

	Combined automated NOESY cross peak assignment and structure calculation:		Combined automated NOESY cross peak assignment and structure calculation:

	* 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)]		* Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA[http://uni-frankfurt.guentert.science/Reprints/Guntert15-NoeassignAlgorithm.pdf .] [http://dx.doi.org/10.1007/s10858-015-9924-9 J. Biomol. NMR 62, 453-471 (2015)]

	* 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[http://~~www.bpc.~~uni-frankfurt.~~de/~~guentert/Reprints/Herrmann02a.pdf .] [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]		* 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[http://uni-frankfurt.guentert.science/Reprints/Herrmann02a.pdf .] [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]

	Evaluation of combined automated NOESY cross peak assignment and structure calculation:		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[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)]		* Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA[http://uni-frankfurt.guentert.science/Reprints/Buchner15-NoeassignEvaluation.pdf .] [http://dx.doi.org/10.1007/s10858-015-9921-z J. Biomol. NMR 62, 81–95 (2015)]