FLYA

Revision as of 11:12, 4 June 2009

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. 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.

Availability

• FLYA calculations are carried out with the program CYANA, using the independent programs NMRView or AUTOPSY, GARANT, and OPALp as additional plug-ins. FLYA is not available as a separate program.

References

• López-Méndez, B. & Güntert, P. Automated protein structure determination from NMR spectra. J. Am. Chem. Soc. 128, 13112-13122 (2006)

Reports or publications of results obtained with FLYA must acknowledge its use by citing this paper.