Influence of non-bonded parameters on the quality of NMR structures: A new force field for NMR structure calculation

Journal of Biomolecular NMR

Volumn 13, Issue 1, 1999, Pages 51-59

  Linge, J P ^a   Nilges, M ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Accuracy; Force fields; Interleukin 4; Precision; Solution structure; Structure validation

Indexed keywords

ARTICLE; CALCULATION; CHEMICAL BOND; COVALENT BOND; CRYSTAL STRUCTURE; FORCE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PARAMETER; PRIORITY JOURNAL; STRUCTURE ANALYSIS; VALIDATION PROCESS;

INTERLEUKIN-4; MATHEMATICAL COMPUTING; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR;

EID: 0033064496     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008365802830     Document Type: Article

References (37)

1. Abagyan, R.A. and Totrov, M.M. (1997) J. Mol. Biol., 268, 678-685.
2. Adams, P.D., Pannu, N.S., Read, R.J. and Brünger, A.T. (1997) Proc. Natl. Acad. Sci. USA, 94, 5018-5023.
3. Allen, F., Brice, M., Cartwright, B., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B., Kennard, O., Motherwell, W., Rodgers, J. and Watson, D. (1979) Acta Crystallogr., B35, 2331-2339.
4. Braun, W. and Gō, N. (1985) J. Mol. Biol., 186, 611-626.
5. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S. and Karplus, M. (1983) J. Comput. Chem., 4, 187-217.
6. Brünger, A.T., Adams, P.D. and Rice, L.M. (1997) Structure, 5, 325-336.
7. Brünger, A. (1992) X-Plor. A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
8. DeLano, W.L. and Brünger, A.T. (1994) Proteins, 20, 105-123.
9. Engh, R. and Huber, R. (1991) Acta Crystallogr., A47, 392-400.
10. Havel, T.F. and Wüthrich, K. (1985) J. Mol. Biol., 182, 281-294.
11. Hendrickson, W.A. (1985) Methods Enzymol., 115, 252-270.
12. Hooft, R.W., Vriend, G., Sander, C. and Abola, E.E. (1996) Nature, 381, 272.
13. Hooft, R.W., Sander, C. and Vriend, G. (1997) Comput. Appl. Biosci., 13, 425-430.
14. Jorgensen, W. and Tirado-Rives, J. (1988) J. Am. Chem. Soc., 110, 1657-1666.
15. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
16. Kuszewski, J., Nilges, M. and Brünger, A.T. (1992) J. Biomol. NMR, 2, 33-56.
17. Kuszewski, J., Gronenborn, A.M. and Clore, G.M. (1996) Protein Sci., 5, 1067-1080.
18. Kuszewski, J., Gronenborn, A. and Clore, G. (1997) J. Magn. Reson., 125, 171-177.
19. Laskowski, R.A., Rullmann, J.A., MacArthur, M.W., Kaptein, R. and Thornton, J.M. (1996) J. Biomol. NMR, 8, 477-486.
20. Müller, T., Dieckmann, T., Sebald, W. and Oschkinat, H. (1994) J. Mol. Biol., 237, 423-436.
21. Müller, T., Oehlenschläger, F. and Buehner, M. (1995) J. Mol. Biol., 247, 360-372.
22. Nilges, M. and O'Donoghue, S. (1998) Progr. NMR Spectrosc., 32, 107-139.
23. Nilges, M., Clore, G.M. and Gronenborn, A.M. (1987) FEBS Lett., 219, 17-21.
24. Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988) FEBS Lett., 239, 129-136.
25. Nilges, M., Kuszewski, J. and Brünger, A.T. (1991) In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, (Hoch, J.C., Poulsen, F.M. and Redfield, C., Eds) Plenum Press, New York, NY, pp. 451-455.
26. Powers, R., Garrett, D.S., March, C.J., Frieden, E.A., Gronenborn, A.M. and Clore, G.M. (1992a) Biochemistry, 31, 4334-4346.
27. Powers, R., Garrett, D.S., March, C.J., Frieden, E.A., Gronenborn, A.M. and Clore, G.M. (1992b) Science, 256, 1673-1677.
28. Prompers, J.J., Folmer, R.H., Nilges, M., Folkers, P.J., Konings, R.N. and Hilbers, C.W. (1995) Eur. J. Biochem., 232, 506-514.
29. Ramachandran, G.N., Ramakrishnan, C. and Sasisekharan, V. (1963) J. Mol. Biol., 7, 95-99.
30. Redfield, C., Boyd, J., Smith, L.J., Smith, R.A. and Dobson, C.M. (1992) Biochemistry, 31, 10431-10437.
31. Sippl, M.J. (1993) Proteins, 17, 355-362.
32. Smith, L.J., Redfield, C., Boyd, J., Lawrence, G.M., Edwards, R.G., Smith, R.A. and Dobson, C.M. (1992) J. Mol Biol., 224, 899-904.
33. Smith, L.J., Redfield, C., Smith, R.A., Dobson, C.M., Clore, G.M., Gronenborn, A.M., Walter, M.R., Naganbushan, T.L. and Wlodawer, A. (1994) Nat. Struct. Biol., 1, 301-310.
34. Stein, E.G., Rice, L.M. and Brünger, A.T. (1997) J. Magn. Reson., 124, 154-164.
35. Vriend, G. (1990) J. Mol. Graph., 8, 52-56.
36. Walter, M.R., Cook, W.J., Zhao, B.G., Cameron Jr., R.P., Ealick, S.E., Walter Jr., R.L., Reichert, P., Nagabhushan, T.L., Trotta, P.P. and Bugg, C.E. (1992) J. Biol. Chem., 267, 20371-20376.
37. Wlodawer, A., Pavlovsky, A. and Gustchina, A. (1992) FEBS Lett., 309, 59-64.