CYANA Publications: Difference between revisions

From CYANA Wiki
Jump to navigation Jump to search
No edit summary
Line 1: Line 1:
== The key publication on SAIL ==
== The key publications on CYANA ==


* Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Ono, A. M. & Güntert, P. Optimal isotope labeling for NMR protein structure determinations. [http://dx.doi.org/10.1038/nature04525 Nature 440, 52–57 (2006)]
* Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. [http://dx.doi.org/10.1006/jmbi.1997.1284 J. Mol. Biol. 273, 283–298 (1997)]  


* 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://dx.doi.org/10.1016/S0022-2836(02)00241-3 J. Mol. Biol. 319, 209–227 (2002)]


== All SAIL-related publications ==
* 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. [http://dx.doi.org/10.1016/0022-2836(91)90754-T J. Mol. Biol. 217, 517–530 (1991)]
 
 
== All CYANA-related publications ==


In reverse chronological order.
In reverse chronological order.


* Terauchi, T., Kobayashi, K., Okuma, K., Oba, M., Nishiyama, K. & Kainosho, M. Stereoselective synthesis of triply isotope-labeled Ser, Cys, and Ala: Amino acids for stereoarray isotope labeling technology. Org. Lett. 10, 2785-2787 (2008)
* Güntert, P. Automated structure determination from NMR Spectra. [http://dx.doi.org/10.1007/s00249-008-0367-z Eur. Biophys. J. (2008)]
 
* Takeda, M., Chang, C. K., Ikeya, T., Güntert, P., Chang, Y. H., Hsu, Y. L., Huang, T. H. & Kainosho, M. Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method. [http://dx.doi.org/10.1016/j.jmb.2007.11.093 J. Mol. Biol. 380, 608–622 (2008)]
 
* 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)]
 
* Scott, A., López-Méndez, B. & Güntert, P. Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. [http://dx.doi.org/10.1002/mrc.1813 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. [http://dx.doi.org/10.1002/mrc.1815 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).


* Takeda, M., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A. M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Güntert, P., Aceti, D. J., Markley, J. L. & Kainosho, M. Structure of the putative 32 kDa myrosinase binding protein from Arabidopsis (At3g16450.1) as determined by the SAIL-NMR method. [http://dx.doi.org/10.1111/j.1742-4658.2008.06717.x FEBS J. 275, 5873–5884 (2008)]
* 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).


* Takeda, M., Chang, C. K., Ikeya, T., Güntert, P., Chang, Y. H., Hsu, Y. L., Huang, T. H. & Kainosho, M. Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method. [http://dx.doi.org/10.1016/j.jmb.2007.11.093 J. Mol. Biol. 380, 608–622 (2008)]
* Herrmann, T., Güntert, P. & Wüthrich, K. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. [http://dx.doi.org/10.1023/A:1021614115432 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. [http://dx.doi.org/10.1016/S0022-2836(02)00241-3 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).


* Ohki, S. Y. & Kainosho, M. Stable Isotope Labeling Methods for Protein NMR Spectroscopy. [http://dx.doi.org/10.1016/j.pnmrs.2008.01.003 Prog. NMR Spectrosc. 53, 208-226 (2008)]
* 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).


* Ikeya, T., Güntert, P. & Kainosho, M. NMRによる蛋白質構造決定の自動化. In 計算シミュレーションと分析データ解析, Maruzen, Tokyo, pp. 148–166 (2007) (in Japanese)
* Güntert, P., Mumenthaler, C. & Wüthrich, K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. [http://dx.doi.org/10.1006/jmbi.1997.1284 J. Mol. Biol. 273, 283–298 (1997)] 


* Takeda, M., Ikeya, T., Güntert, P. & Kainosho, M. Automated structure determination of proteins with the SAIL-FLYA NMR method. [http://dx.doi.org/10.1038/nprot.2007.423 Nature Protocols 2, 2896–2902 (2007)]
* Güntert, P. Calculating protein structures from NMR data. Meth. Mol. Biol. 60, 157–194 (1997).


* Ikeya, T., Terauchi, T., Güntert, P., Kainosho, M. Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA. [http://dx.doi.org/10.1002/mrc.1815 Magn. Reson. Chem. 44, S152–S157 (2006)]
* 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).


* Kainosho, M. & Güntert, P. 高分子量タンパク質のNMR構造決定-より速く、より正確に: タンパク質NMRの常識を覆す革新技術SAIL法. Stereo-array isotope labeling for faster and more accurate NMR structure determinations of high molecular weight proteins. Biotechnology J. (Tokyo) 6, 467–470 (2006) (in Japanese)
* 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).


* Kainosho, M., Torizawa, T., Iwashita, Y., Terauchi, T., Ono, A. M. & Güntert, P. Optimal isotope labeling for NMR protein structure determinations. [http://dx.doi.org/10.1038/nature04525 Nature 440, 52–57 (2006)]
* Güntert, P. Neue Rechenverfahren für die Proteinstrukturbestimmung mit Hilfe der magnetischen Kernspinresonanz, Ph.D. Thesis ETH 10135 [http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10135 (1993)]


* Opella, S. J. Designer labels. [http://dx.doi.org/10.1038/440040a Nature 440, 40 (2006)]
* 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).


* Torizawa, T., Ono, A. M., Terauchi, T. & Kainosho, M. (2005). NMR assignment methods for the aromatic ring resonances of phenylalanine and tyrosine residues in proteins. J. Am. Chem. Soc. 127, 12620-12626.
* 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. [http://dx.doi.org/10.1016/0022-2836(91)90754-T J. Mol. Biol. 217, 517–530 (1991)]


* Torizawa, T., Shimizu, M., Taoka, M., Miyano, H. & Kainosho, M. Efficient production of isotopically labeled proteins by cell-free synthesis: A practical protocol. J. Biomol. NMR 30, 311-325 (2004)
* 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).


* Sugimori, N., Torizawa, T., Aceti, D. J., Thao, S., Markley, J. L. & Kainosho, M. Letter to the Editor: <sup>1</sup>H, <sup>13</sup>C and <sup>15</sup>N backbone assignment of a 32 kDa hypothetical protein from Arabidopsis thaliana, At3g16450.1. J. Biomol. NMR 30, 357-358 (2004)
* Güntert, P., Braun, W., Billeter, M. & Wüthrich, K. Automated stereospecific <sup>1</sup>H NMR assignments and their impact on the precision of protein structure determinations in solution. J. Amer. Chem. Soc. 111, 3997–4004 (1989).


== Further publications ==
== Further publications ==


* [[Publications of M. Kainosho|All Publications of M. Kainosho]]
[[Publications of P. Güntert|All Publications of P. Güntert]]
* [[Publications of P. Güntert|All Publications of P. Güntert]]

Revision as of 17:35, 7 January 2009

The key publications on CYANA

  • 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., 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.

  • Takeda, M., Chang, C. K., Ikeya, T., Güntert, P., Chang, Y. H., Hsu, Y. L., Huang, T. H. & Kainosho, M. Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein determined by the SAIL-NMR method. J. Mol. Biol. 380, 608–622 (2008)
  • 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. 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. Amer. Chem. Soc. 111, 3997–4004 (1989).

Further publications

All Publications of P. Güntert

Retrieved from "https://cyana.org/w/index.php?title=CYANA_Publications&oldid=551"