CYANA Publications

The key publications on CYANA

• Klukowski, P., Riek, R. & Güntert, P. Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA. Nat. Commun. 13, 6151 (2022)

• Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453-471 (2015)

• Schmidt, E. & Güntert, P. A new algorithm for reliable and general NMR resonance assignment. J. Am. Chem. Soc. 134, 12817–12829 (2012)

• 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. 319, 209–227 (2002)

• Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298 (1997)

• Güntert, P., Braun, W. & Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517–530 (1991)

All CYANA-related publications

In reverse chronological order.

• Klukowski, P., Riek, R. & Güntert, P. Time-optimized protein NMR assignment with an integrative deep learning approach using AlphaFold and chemical shift prediction. Sci. Adv. 9, eadi9323 (2023)

• Wetton, H, Klukowski, P., Riek, R. & Güntert, P. Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA. Front. Mol. Biosci. 10, 1244029 (2023)

• Kuschert, S., Stroet, M., Chin, Y. K. Y., Conibear, A. C., Jia, X., Lee, T., Bartling, C. R. O., Strømgaard, K., Güntert, P., Rosengren, K. J., Mark, A. E. & Mobli, M. Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. Magn. Reson. 4, 57-72 (2023)

• Klukowski, P., Riek, R. & Güntert, P. NMRtist: an online platform for automated biomolecular NMR spectra analysis. Bioinformatics 39, btad066 (2023)

• Klukowski, P., Riek, R. & Güntert, P. Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA. Nat. Commun. 13, 6151 (2022)

• Cucuzza, S., Güntert, P., Plückthun, A. & Zerbe, O. An automated iterative approach for protein structure refinement using pseudocontact shifts. J. Biomol. NMR 75, 319-334 (2021)

• Pritišanac, I., Alderson, T. R. & Güntert, P. Automated assignment of methyl NMR spectra from large proteins. Prog. NMR Spectrosc. 118–119, 54–73 (2020)

• Pritišanac, I., Würz, J. M., Alderson, T. R., Güntert, P. Automatic structure-based NMR methyl resonance assignment in large proteins. Nat. Commun. 10, 4922 (2019)

• Pritišanac, I., Würz, J. M. & Güntert, P. Fully automated assignment of methyl resonances of a 36 kDa protein dimer from sparse NOESY data. J. Phys Conf. Ser. 1036, 012008 (2018)

• Würz, J. M., Kazemi, S., Schmidt, E., Bagaria, A. & Güntert, P. NMR-based automated protein structure determination. Arch. Biochem. Biophys. 628, 24-32 (2017)

• Würz, J. M. & Güntert, P. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK. J. Biomol. NMR. 67, 63–76 (2017)

• Kazemi, S., Würz, J. M., Schmidt, E., Bagaria, A. & Güntert, P. Automated structure determination from NMR spectra. In Modern Magnetic Resonance 2nd Ed. (Ed. G. Webb), Springer.

• Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary. J. Biomol. NMR 63, 21-37 (2015)

• Güntert, P. & Buchner, L. Combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 453-471 (2015)

• Buchner, L. & Güntert, P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J. Biomol. NMR 62, 81–95 (2015)

• Buchner, L. & Güntert, P. Increased reliability of NMR protein structures by consensus structure bundles. Structure 23, 425–434 (2015)

• Schmidt, E. & Güntert, P. Automated structure determination from NMR spectra. Meth. Mol. Biol. 1261, 303–329 (2015)

• Lin, Y. J., Ikeya, T., Kirchner, D. K. & Güntert, P. Influence of incomplete NOESY peaks of the interface residues on structure determinations of homodimeric proteins. J. Chin. Chem. Soc. 61, 1297-1306 (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. J. Biomol. NMR 59, 87-93 (2014)

• Orts, J., Vögeli, B., Riek, R. & Güntert, P. Stereospecific assignments in proteins using exact NOEs. J. Biomol. NMR 57, 211-218 (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)

• Schmidt, E. & Güntert, P. Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins. J. Biomol. NMR 57, 193-204 (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. J. Biomol. NMR 56, 243–254 (2013)

• Buchner, L., Schmidt, E. & Güntert, P. Peakmatch: a simple and robust method for peak list matching. J. Biomol. NMR. 55, 267–277 (2013)

• Vögeli, B., Güntert, P., & Riek, R. Multiple-state ensemble structure determination from eNOE spectroscopy. Mol. Phys. 111, 437–454 (2013)

• Vögeli, B., Kazemi, S., Güntert, P. & Riek, R. Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs. Nature Struct. Mol. Biol. 19, 1053–1057 (2012)

• Gottstein, D., Kirchner, D. K. & Güntert, P. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. J. Biomol. NMR 52, 351-364 (2012)

• Rosato, A., Aramini, J. M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers, J. F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Güntert, P., He. Y. F., Herrmann, T., Huang, Y. J., Jaravine, V., Jonker, H. R. A., Kennedy, M. A., Lange, O. F., Liu, G., Malliavin, T. E., Mani, R., Mao, B., Montelione, G. T., Nilges, M., Rossi, P., van der Schot, G., Schwalbe, H., Szyperski, T., Vendruscolo, M., Vernon, R., Vranken, W. F., de Vries, S., Vuister, G. W., Wu, B. Yang, Y. & Bonvin, A. M. J. J. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20, 227–236 (2012)

• Güntert, P. Calculation of structures from NMR restraints. In Protein NMR Spectroscopy: Practical Techniques and Applications (Eds. G. Roberts & L.-Y. Lian), Wiley, New York, pp. 159–192 (2011).

• Kirchner, D. K. & Güntert, P. Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12, 170 (2011)

• Ikeya, T., Jee. J. G., Shigemitsu, Y., Hamatsu, J., Mishima, M., Ito, Y., Kainosho, M. & Güntert, P. Exclusively NOESY-based automated NMR assignment and structure determination of proteins. J. Biomol. NMR. 50, 137–146 (2011)

• Güntert, P. Automated structure determination from NMR spectra. In Advances in Biomedical Spectroscopy. Volume 3: Biomolecular NMR Spectroscopy (Eds. A. Dingley & S. Pascal), IOS Press, Amsterdam, pp. 338–365 (2011)

• Hefke, F., Bagaria, A., Reckel, S., Ullrich, S.J., Dötsch, V., Glaubitz, C. & Güntert P. Optimization of amino acid type-specific ¹³C and ¹⁵N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm. J. Biomol. NMR 49, 75-84 (2011)

• Kainosho, M. & Güntert, P. SAIL – Stereo-array isotope labeling. Q. Rev. Biophys. 42, 247-300 (2009)

• Ikeya, T., Takeda, M., Yoshida, H., Terauchi, T., Jee, J., Kainosho, M. & Güntert, P. Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system. J. Biomol. NMR. 44, 261-272 (2009)

• Güntert, P. Automated structure determination from NMR Spectra. Eur. Biophys. J. 38, 129-143 (2009)

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

• Scott, A., López-Méndez, B. & Güntert, P. Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. Magn. Reson. Chem. 44, S83–S88 (2006)

• Ikeya, T., Terauchi, T., Güntert, P., Kainosho, M. Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA. Magn. Reson. Chem. 44, S152–S157 (2006)

• Güntert, P. Automated NMR structure calculation with CYANA. Meth. Mol. Biol. 278, 353–378 (2004)

• Güntert, P. Automated NMR protein structure calculation. Prog. NMR Spectrosc. 43, 105–125 (2003)

• Jee, J. G. & Güntert, P. Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J. Struct. Funct. Genom. 4, 179–189 (2003)

• 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 24, 171–189 (2002)

• Güntert, P. Structure calculation using automated techniques. Meth. Principles Med. Chem. 16, 39–66 (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. J. Mol. Biol. 319, 209–227 (2002)

• Güntert, P. & Wüthrich, K. Sampling of conformation space in torsion angle dynamics calculations. Comp. Phys. Commun. 138, 155–169 (2001)

• Güntert, P., Billeter, M., Ohlenschläger, O., Brown, L. & Wüthrich, K. Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND. J. Biomol. NMR 12, 543–548 (1998)

• Banci, L., Bertini, I., Cremonini, M. A., Gori-Savellini, G., Luchinat, C., Wüthrich, K. & Güntert, P. PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics.J. Biomol. NMR 12, 553–557 (1998)

• Güntert, P. Structure calculation of biological macromolecules from NMR data. Q. Rev. Biophys. 31, 145–237 (1998)

• Mumenthaler, C., Güntert, P., Braun, W. & Wüthrich, K. Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J. Biomol. NMR 10, 351–362 (1997)

• Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283–298 (1997)

• Güntert, P. Calculating protein structures from NMR data. Meth. Mol. Biol. 60, 157–194 (1997).

• Güntert, P. Computer–supported protein structure determination by NMR. In Statistical mechanics, protein structure and protein–substrate interactions (Ed. S. Doniach), Plenum Press, New York, pp. 197–207 (1994).

• Güntert, P., Berndt, K. D. & Wüthrich, K. The program ASNO for computer-supported collection of NOE upper distance constraints as input for protein structure determination. J. Biomol. NMR 3, 601–606 (1993)

• Güntert, P. Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz, Ph.D. Thesis ETH 10135 (1993)

• Güntert, P. & Wüthrich, K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR 1, 447–456 (1991)

• Güntert, P., Braun, W. & Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517–530 (1991)

• Güntert, P., Qian, Y. Q., Otting, G., Müller, M., Gehring, W. J. & Wüthrich K. Structure determination of the Antp(C39S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 531–540 (1991)

• Güntert, P., Braun, W., Billeter, M. & Wüthrich, K. Automated stereospecific ¹H NMR assignments and their impact on the precision of protein structure determinations in solution. J. Am. Chem. Soc. 111, 3997–4004 (1989)

Further publications

All Publications of P. Güntert