Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

Journal of Computational Chemistry

Volumn 18, Issue 12, 1997, Pages 1450-1462

  Bartels, Christian ^a   Karplus, Martin ^b  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Adaptive umbrella sampling; Main chain; Peptide conformations; Side chain

Indexed keywords

EID: 4344606960     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199709)18:12<1450::AID-JCC3>3.0.CO;2-I     Document Type: Article

References (37)

1. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics, Wiley, New York, 1988.
2. J. A. McCammon and S. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, U.K., 1987.
3. T. Lazaridis, C. L. Brooks III, and M. E. Paulaitis, J. Chem. Phys., 95, 7612 (1991).
4. G. M. Torrie and J. P. Valleau, J. Comput. Phys., 23, 187 (1977).
5. J. P. Valleau and G. M. Torrie, In Statistical Mechanics, Part A: Equilibrium Techniques, B. J. Berne, Ed., Plenum Press, New York, 1977, p. 169.
6. S. H. Northrup, M. R. Pear, C.-Y. Lee, J. A. McCammon, and M. Karplus, Proc. Natl. Acad. Sci. USA, 79, 4035 (1982).
7. M. Mezei, J. Comput. Phys., 68, 237 (1987).
8. T. C. Beutler, Ph.D. thesis, ETH, Zürich, 1994.
9. G. H. Paine and H. A. Scheraga, Biopolymers, 24, 1391 (1985).
10. R. W. W. Hooft, B. P. van Eijck, and J. Kroon, J. Chem. Phys., 97, 6690 (1992).
11. A. M. Ferrenberg, Ph.D. thesis, Carnegie-Mellon University, Pittsburgh, PA, 1989.
12. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem., 13, 1011 (1992).
13. E. M. Boczko and C. L. Brooks III, J. Phys. Chem., 97, 4509 (1993).
14. J. Lee, Phys. Rev. Lett., 71, 211 (1993).
15. A. Kidera, Proc. Natl. Acad. Sci. USA, 92, 9886 (1995).
16. M.-H. Hao and H. A. Scheraga, J. Phys. Chem., 98, 4940 (1994).
17. B. A. Berg, Int. J Modern Phys., C3, 1083 (1992).
18. B. A. Berg and T. Neuhaus, Phys. Rev. Lett., 68, 9 (1992).
19. U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem., 14, 1333 (1993).
20. U. H. E. Hansmann and Y. Okamoto, Physica A, 212, 415 (1994).
21. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys., 96, 1776 (1992).
22. C. Bartels and M. Karplus, manuscript in preparation.
23. R. L. J. Dunbrack, Ph.D. thesis, Harvard University, Cambridge, MA, 1993.
24. R. L. J. Dunbrack and M. Karplus, J. mol. Biol., 230, 543 (1993).
25. A. G. Anderson and J. Hermans, Proteins Struct. Fund. Genet., 3, 262 (1988).
26. D. J. Tobias and C. L. Brooks III, J. Phys. Chem., 96, 3864 (1992).
27. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in Fortran, The Art of Scientific Computing, Cambridge University Press, Cambridge, U.K., 1986.
28. I. N. Bronstein and K. A. Semendjajew, Taschenbuch der Mathematik, Verlag Harri Deutsch, Thun, Switzerland, 1989.
29. U. Krengel, Einführung in die Wahrscheinlichkeitstheorie und Statistik, Vieweg, Braunschweig/Wiesbaden, Germany, 1991.
30. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983).
31. A. D. MacKerell, Jr. et al., FASEB J., 6, A143 (1992).
32. A. D. MacKerell, Jr. et al., manuscript in preparation.
33. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys., 23, 327 (1977).
34. T. C. Beutler and W. F. van Gunstern, Chem. Phys. Lett., 237, 308 (1995).
35. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem., 16, 1339 (1995).
36. T. C. Beutler, T. Bremi, R. R. Ernst, and W. F. van Gunstern, J. Phys. Chem., 100, 2637 (1996).
37. S. Kumar, P. W. Payne, and M. Vásquez, J. Comput. Chem., 17, 1269 (1996).