PROSHIFT: Protein chemical shift prediction using artificial neural networks

Journal of Biomolecular NMR

Volumn 26, Issue 1, 2003, Pages 25-37

  Meiler, Jens ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

Chemical shift prediction; Neural Networks; NMR; Proteins

Indexed keywords

CARBON 13; NITROGEN 15; PROTON;

ARTIFICIAL NEURAL NETWORK; ATOM; COMPUTER PROGRAM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DATA BASE; MOLECULAR SIZE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTITATIVE ANALYSIS; REVIEW; STRUCTURE ANALYSIS; VALIDATION PROCESS;

AMINO ACID SEQUENCE; CARBON ISOTOPES; DATABASES, FACTUAL; HYDROGEN; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NERVE NET; NITROGEN ISOTOPES; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 0038703404     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1023060720156     Document Type: Review

References (46)

1. Bonneau, R., Tsai, J., Ruczinski, I., Chivian, D., Rohl, C., Strauss, C. E. M. and Baker, D. (2001) Proteins, 45 (Suppl.), 119-126.
2. Braun, D., Wider, G. and Wucthrich, K. (1994) J. Am. Chem. Soc., 116, 8466-8469.
3. Chandonia. J.-M. and Karplus, M. (1999) Proteins Struct. Funct. Genet., 35, 293-306.
4. Choy, W.Y.. Sanctuary, B.C. and Zhu, G. (1997) J. Chem. Inf. Comput. Sci., 37, 1086-1094.
5. Clouser, D.L. and Jurs, P.C. (1996) Anal. Chim. Acta, 321, 127-135.
6. Cornilescu, G., Delaglio, F. and Bax, A. (1999) J. Biomol. NMR, 13, 289-302.
7. Gronwald, W., Boyko, R.F., Sonnichsen, F.D., Wishart, D.S. and Sykes, B.D. (1997) J. Biomol. NMR, 10, 165-179.
8. Ivanciue, O., Rabine, J.P., Cabrol-Bass, D., Panaye, A. and Doueet, J.-P. (1996) J. Chem. Inf. Comput. Sci., 36, 644-653.
9. Iwadate, M., Asakura, T. and Williamson, M.P. (1999) J. Biomol. NMR, 13, 199-211.
10. Jones, D.T. (1999) J. Mol. Biol., 292, 195-202.
11. Kneller, D.G., Cohen, F.E. and Langridge, R. (1990) J. Mol. Biol., 214, 171-182.
12. Kvasnicka, V., Sklenak, S. and Pospichal, J. (1992) J. Chem. Inf. Comput. Sci., 32, 742-747.
13. Le, H. and Oldfield, E. (1994) J. Biomol. NMR, 4, 341-348.
14. Luman, N.R., King, M.P. and Augspurger. J.D. (2001) J. Comput. Chem., 22, 366-372.
15. Meiler, J. (1996-2002) www.jens-meiler.de
16. Meiler, J. (2002a) www.jens-meiler.de/jufo.html
17. Meiler, J. (2002b) www.jens-meiler.de/proshift.html
18. Meiler, J. and Will, M. (2001) J. Chem. Inf. Comput. Sci., 41. 1535-1546.
19. Meiler, J., Maier, W., Will, M. and Meusinger, R. (2002) J. Magn. Reson., 157, 242-252.
20. Meiler, J., Müller, M., Zeidler, A. and Schmäschke, F. (2001) J. Mol. Model., 7, 360-369.
21. Meiler, J., Will, M. and Meusinger, R. (2000) J. Chem. Inf. Comput. Sci., 40, 1169-1176.
22. Meusinger, R. and Moros, R. (1995) In Software - Entwicklung in der Chemie, Vol. 10, Gasteiger, J., Ed. Gesellschaft Deutscher Chemiker, Frankfurt am Main, pp. 209-216.
23. Oldfield, E. (1995) J. Biomol. NMR, 5, 217-225.
24. Osapay, K. and Case, D.A. (1991) J. Am. Chem. Soc., 113, 9436-9444.
25. Pearson, J.G., Le, H., Sanders, L.K., Godbout, N., Havlin, R.H. and Oldfield, E. (1997) J. Am. Chem. Soc., 119, 11941-11950.
26. Petersen, T.N., Lundegaard, C., Nielsen, M., Bohr, H., Bohr, J., Brunak, S., Gippert, G.P. and Lund, O, (2000) Proteins Struct. Funct. Genet., 41, 17-20.
27. Pons, J.L. and Delsuc, M.A. (1999) J. Biomol. NMR, 15, 15-26.
28. Qian, N. and Sejnowski, T.J. (1988) J. Mol. Biol., 202, 865-884.
29. Ramirez, B.E., Voloshin, O.N., Camerim-Otero, R.D. and Bax, A. (2000) Protein Sci., 9, 2161.
30. Robien, W. (1998) Nachr. Chem. Tech. Lab., 46, 74-77.
31. Rohl, C. and Baker, D. (2002) J. Am. Chem. Soc., 124, 2723-2729.
32. Rost, B. (1996) Meth. Enzymol., 266, 525-539.
33. Rost, B. and Sander, C. (1993) J. Mol. Biol., 232, 584-599.
34. Rost, B., Sander, C. and Schneider, R. (1994) J. Mol. Biol., 235, 13-26.
35. Salamov, A.A. and Solovyev, V.V. (1997) J. Mol. Biol., 268, 31-36.
36. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490-5492.
37. Stolorz, P., Lapedes, A. and Xia, Y. (1992) J. Mol. Biol., 225, 363-377.
38. Thomas, S. and Kleinpeter, E. (1995) J. Prakt. Chem./Chem.-Zig., 337, 504-507.
39. Wang, Y. and Jardetzky, O. (2002) Protein Sci., 11, 852-861.
40. Wishart, D.S. and Sykes, B.D. (1994) J. Biomol. NMR, 4, 171-180.
41. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995) J. Biomol. NMR, 5, 67-81.
42. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647-1651.
43. Wishart, D.S., Watson, M.S., Boyko, R.F. and Sykes, B.D. (1997) J. Biomol. NMR, 10, 329-336.
44. lH-NMR Shifts of Amino Acids), John Wiley & Sons, New York, Chichester, Brisbane, Toronto, Singapore.
45. Xu, X.-P. and Case, D.A. (2001) J. Biomol. NMR, 21, 321-333.
46. Zupan, J. and Gasteiger, J. (1993) Neural Networks for Chemists, VCH Verlagsgesellschaft mbH. Weinheim.