Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

Journal of Biomolecular NMR

Volumn 26, Issue 3, 2003, Pages 215-240

  Neal, Stephen ^a   Nip, Alex M ^a   Zhang, Haiyan ^a   Wishart, David S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Calculation; Chemical shift; Data mining; NMR; Prediction; Protein

Indexed keywords

CARBON 13; NITROGEN 15; PROTON; SOLVENT;

ACCURACY; ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; COMPUTER PROGRAM; CONTROLLED STUDY; CRYSTAL STRUCTURE; DATA BASE; ELECTRIC FIELD; GEOMETRY; HYDROGEN BOND; MAGNETIC FIELD; NITROGEN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SENSITIVITY ANALYSIS; X RAY CRYSTALLOGRAPHY;

ANIMALS; CARBON ISOTOPES; HUMANS; HYDROGEN; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; SOFTWARE;

EID: 0038407231     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023812930288     Document Type: Article

References (48)

1. Baker, E.N. and Hubbard, R.E. (1984) Prog. Biophys. Mol. Biol., 44, 97-179.
2. Banci, L., Bertini, L, Savellini, G.G., Romagnoli, A., Turano, P., Cremonini, M.A., Luchinat, C. and Gray, H.B. (1997) Prot. Struct. Funct. Gen., 29, 68-76.
3. Baxter, N.J. and Williamson, M.P. (1997) J. Biomol. NMR, 9, 359-369.
4. Beger, R.D. and Bolton, P.H. (1997) J. Biomol. NMR, 10, 129-142.
5. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucl. Acids Res., 28, 235-242.
6. Bjorndahl, T.C., Watson, M.S., Slupsky, C.M., Spyracopolous, L., Sykes, B.D. and Wishart, D.S. (2001) J. Biomol. NMR, 19, 187-188.
7. Braun, D., Wider, G. and Wüthrich, K. (1994) J. Am. Chem. Soc., 116, 8466-8469.
8. Buckingham, A.D. (1960) Can. J. Chem., 38, 300-307.
9. Case, D.A. (1998) Curr. Opin. Struct. Biol., 8, 624-630.
10. Case, D.A. (2000) Curr. Opin. Struct. Biol., 10, 197-203.
11. Cornilescu, G., Delaglio, F. and Bax, A. (1999) J. Biomol. NMR, 13, 289-302
12. Dalgarno, D.C., Levine, B.A. and Williams, R.J.P. (1983) Biosci. Rep., 3, 443-452.
13. de Dios, A.C., Pearson, J.G. and Oldfield, E. (1993) Science, 260, 1491-1496.
14. Derewenda, Z.S., Lee, L. and Derewenda, U. (1995) J. Mol. Biol. 252, 248-262.
15. Doreleijers, J.F., Rullmann, J.A. and Kaptein, R. (1998) J. Mol. Biol., 281, 149-164.
16. Gardner, K.H., Rosen, M. K. and Kay, L.E. (1997) Biochemistry, 36, 1389-1401.
17. Gibas, C.J. and Subramanian, S. (1996) Biophys. J. 71, 130-147.
18. Haigh, C.W. and Mallion, R.B. (1980) Progr. NMR Spectrosc., 13, 303-344.
19. Herranz, J., Gonzalez, C., Rico, M., Nieto, J.L., Santoro, J., Jimenez, M.A., Bruix, M., Neira, J.L. and Blanco, F.J. (1992) Magn. Reson. Chem., 30, 1012-1018.
20. Iwadate, M., Asakura, T. and Williamson, M.P. (1999) J. Biomol. NMR, 13, 199-211.
21. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
22. Kuszewski, J., Qin, J., Gronenborn, A.M. and Clore, G.M. (1995a) J. Magn. Reson. B., 106, 92-96.
23. Kuszewski, J., Gronenborn, A.M. and Clore, G.M. (1995b) J. Magn. Reson., B107, 293-297.
24. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J. Biomol. NMR, 8, 477-486.
25. Le, H. and Oldfield, E. (1994) J. Biomol. NMR, 4, 341-348.
26. Le, H., Pearson, J.G., de Dios, A.C. and Oldfield, E. (1995). J. Am. Chem. Soc. 117, 3800-3807.
27. Markley, J.L., Bax, A., Arata, Y, Hilbers, C.W., Kaptein, R., Sykes, B.D., Wright, P.E. and Wüithrich, K. (1998) J. Biomol. NMR, 12, 1-23.
28. Osapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436-9444.
29. Osapay, K. and Case, D.A. (1994) J. Biomol. NMR, 4, 215-230.
30. Osapay, K., Theriault, Y., Wright, P.E. and Case, D.A. (1994) J. Mol. Biol., 244, 183-197.
31. Pearson, J.T., Le, H., Sanders, L.K., Godbout, N., Havlin, R.H. and Oldfield, E. (1997) J. Am. Chem. Soc. 119, 11941-11950.
32. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol. NMR, 1, 217-236.
33. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490-5492.
34. Wagner, G., Pardi, A. and Wüthrich, K. (1983) J. Am. Chem. Soc., 105, 5948.
35. Williamson, M.P. and Asakura, T. (1997) Meth. Mol. Biol., 60, 53-69.
36. Williamson, M.P., Asakura, T., Nakamura, E. and Demura, M. (1992) J. Biomol. NMR, 2, 93-98.
37. Williamson, M.P., Kikuchi, J. and Asakura, T. (1995) J. Mol. Biol., 247, 541-546.
38. Wishart, D.S. and Case, D.A. (2001) Meth. Enzymol., 338, 3-34.
39. Wishart, D.S. and Nip, A.M. (1998) Biochem. Cell Biol., 76, 153-163.
40. Wishart, D.S. and Sykes, B.D. (1994) Meth. Enzymol., 239, 363-392.
41. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995a) J. Biomol. NMR, 5, 67-81.
42. Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L. and Sykes, B.D. (1995b) J. Biomol. NMR, 6, 135-140.
43. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J. Mol. Biol., 222, 311-333.
44. Wishart, D.S., Willard, L., Richards, F.M. and Sykes, B.D. (1994) VADAR: A comprehensive program for protein structure evaluation. Version 1.2. Edmonton, Alberta, Canada.
45. Word, J.M., Lovell, S.C., Richardson, J.S. and Richardson, D.C. (1999) J. Mol. Biol., 285, 1733-1747.
46. Xu, X-P. and Case, D.A. (2001) J. Biomol. NMR, 21, 321-333.
47. Xu, X-P. and Case, D.A. (2002) Biopolymers, 65, 408-423.
48. Zhang, H., Neal, S. and Wishart, D.S. (2003) J. Biomol. NMR, 25, 173-195.