FINGAR: A new genetic algorithm-based method for fitting NMR data

Journal of Biomolecular NMR

Volumn 8, Issue 1, 1996, Pages 49-66

  Pearlman, David A ^a  

^a VERTEX PHARMACEUTICALS   (United States)

Author keywords

Adenosine; FK506; Genetic algorithm; Refinement

Indexed keywords

EID: 0001843949     PISSN: 09252738     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00198139     Document Type: Article

References (50)

1. Altona, C. and Sundaralingam, M. (1972) J. Am. Chem. Soc., 94, 8205-8212.
2. Atkins, P.W. (1990) Physical Chemistry, Freeman, New York, NY.
3. Bonvin, A.M.J.J. and Brunger, A.T. (1995) J. Mol. Biol., 250, 80-93.
4. Bonvin, A.M.J.J. and Brunger, A.T. (1996) J. Biomol. NMR, 7, 72-76.
5. Borgias, B.A. and James, T.L. (1988) J. Magn. Reson., 79, 493-512.
6. Brunger, A.T. and Karplus, M. (1991) Acc. Chem. Reson., 24, 54-61.
7. Brunger, A.T., Clore, G.M., Gronenborn, A.M., Saffrich, R. and Nilges, M. (1993) Science, 261, 328-331.
8. Bruschweiler, R., Blackledge, M. and Ernst, R.R. (1991) J. Biomol. NMR, 1, 3-11.
9. Burkert, U. and Allinger, N.L. (1982) Molecular Mechanics, American Chemical Society Monographs, Vol. 177, American Chemical Society, Washington, D.C.
10. Clore, G.M., Nilges, M., Sukumaran, D.K., Brunger, A.T., Karplus, M. and Gronenborn, A.M. (1986) EMBO J., 5, 2729-2735.
11. Crippen, G.M. and Havel, T.F. (1988) Distance Geometry and Molecular Conformation, Wiley, New York, NY.
12. Davies, D.B. (1978) Prog. NMR Spectrosc., 12, 135-225.
13. Fennen, J., Torda, A.E. and Van Gunsteren, W.F. (1995) J. Biomol. NMR, 6, 163-170.
14. Goldberg, D.E. (1989) Genetic Algorithms in Search, Optimization, and Machine Learning, Addison Wesley, Reading, MA.
15. Gonzalez, C., Stec, W., Reynolds, M.A. and James, T.L. (1995) Biochemistry, 34, 4969-4982.
16. Havel, T.F. (1990) Biopolymers, 29, 1565-1585.
17. Karplus, M. (1959) J. Chem. Phys., 30, 11-15.
18. Kemmink, J. and Scheek, R.M. (1995) J. Biomol. NMR, 5, 33-40.
19. Kessler, H., Griesinger, C., Lautz, J., Muller, A., Van Gunsteren, W.F. and Berendsen, H.J.C. (1988) J. Am. Chem. Soc., 110, 3393-3396.
20. Kim, S.-G., Lin, L.-J. and Reid, B.R. (1992) Biochemistry, 31, 3564-3574.
21. Kim, Y. and Prestegard, J.H. (1990) Protein Struct. Funct. Genet., 8, 377-385.
22. Landis, C. and Allured, Y.S. (1991) J. Am. Chem. Soc., 113, 9493-9499.
23. Landis, C.R., Luck, L.L. and Wright, J.M. (1995) J. Magn. Reson., 109, 44-59.
24. Lawson, C.L. and Hanson, R.J. (1974) Solving Least-Squares Problems, Prentice-Hall, New York, NY.
25. Lepre, C.A., Thomson, J.A. and Moore, J.M. (1992) FEBS Lett., 302, 89-96.
26. Massart, D.L. and Kaufman, L. (1983) The Interpretation of Analytical Chemical Data by the Use of Cluster Analysis, Wiley, New York, NY.
27. Nanzer, A.P., Van Gunsteren, W.F. and Torda, A.E. (1995) J. Biomol. NMR, 6, 313-320.
28. Nikiforovich, G.V., Prakash, O., Gehrig, C.A. and Hruby, V.J. (1993) J. Am. Chem. Soc., 115, 3399-3406.
29. Nilges, M., Clore, G.M. and Gronenborn, A.M. (1988) FEBS Lett., 229, 317-324.
30. Nilges, M., Habazettl, J., Brunger, A.T. and Holak, T.A. (1991) J. Mol. Biol., 219, 499-510.
31. Pearlman, D.A. and Kollman, P.A. (1991) J. Mol. Biol., 220, 457-479.
32. Pearlman, D.A. (1994a) J. Biomol. NMR, 4, 1-16.
33. Pearlman, D.A. (1994b) J. Biomol. NMR, 4, 279-299.
34. Pearlman, D.A., Case, D.A., Caldwell, J.C., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D.M., Seibel, G.L. and Kollman, P.A. (1995) Comput. Phys. Commun., 91, 1-41.
35. Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1989) Numerical Recipes, Cambridge University Press, New York, NY.
36. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer, New York, NY.
37. Scheek, R.M., Van Nuland, N.A.J., De Groot, B.L. and Amadei, A. (1995) J. Biomol. NMR, 5, 106-111.
38. Schmitz, U., Ulyanov, N.B., Kumar, A. and James, T.L. (1993) J. Mol. Biol., 234, 373-389.
39. Schreiber, S.L. (1991) Science, 251, 283-287.
40. Torda, A.E., Scheek, R.M. and Van Gunsteren, W.F. (1989) Chem. Phys. Lett., 157, 289-294.
41. Torda, A.E., Scheek, R.M. and Van Gunsteren, W.F. (1990) J. Mol. Biol., 214, 223-235.
42. Torda, A.E., Brunne, R.M., Huber, T., Kessler, H. and Van Gunsteren, W.F. (1993) J. Biomol. NMR, 3, 55-66.
43. Tropp, J. (1980) J. Chem. Phys., 72, 6035-6043.
44. Ulyanov, N.B., Schmitz, U., Kumar, A. and James, T.L. (1995) Biophys. J., 68, 13-24.
45. Van de Ven, F.J.M. and Hilbers, C.W. (1988) Eur. J. Biochem., 178, 1-38.
46. Van Gunsteren, W.F., Brunne, R.M., Gros, P., Van Schaik, R.C., Schiffer, C.A. and Torda, A.E. (1994) Methods Enzymol., 239, 619-654.
47. Wagner, G. and Wüthrich, K. (1979) J. Magn. Reson., 33, 675-680.
48. Wüthrich, K. (1990) J. Biol. Chem., 265, 22059-22062.
49. Yang, J.-X. and Havel, T.F. (1993) J. Biomol. NMR, 3, 355-360.
50. Yip, P. and Case, D.A. (1989) J. Magn. Reson., 83, 643-648.