Predicting Helical Hairpins from Sequences by Monte Carlo Simulations

Journal of Computational Chemistry

Volumn 21, Issue 7, 2000, Pages 582-589

  Derreumaux, Philippe ^a,b  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^b CNRS   (France)

Author keywords

Ab initio structure prediction; Global optimization; Monte Carlo simulations; Optimized potential; helical hairpins

Indexed keywords

EID: 0000035533     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(200005)21:7<582::AID-JCC7>3.0.CO;2-T     Document Type: Article

References (32)

1. Anfinsen, C. B. Science 1973, 181, 223-230.
2. Levitt, M.; Warshel, A. Nature 1975, 253, 694-698.
3. Taketomi, H.; Ueda, Y.; Go, N. Int J Pept Prot Res 1975, 7, 445-459.
4. (a) Lecomte, J. T. J.; Falzone, C. J. Nature Struct Biol 1999, 6, 605-608;
5. (b) Sabelko, J.; Ervin, J.; Gruebele, M. Proc Natl Acad Sci USA 1999, 96, 6031-6036.
6. (a) Tuchscherer, G.; Scheiber, L.; Dumy, P.; Mutter, M. Biopolymers (Pept Sci) 1998, 47, 63-73;
7. (b) Walsh, S. T. R., et al., Proc Natl Acad Sci USA 1999, 96, 5486-5491.
8. (a) Dinner, A. R.; So, S.-S.; Karplus, M. Prot Struct Funct Genet 1998, 33, 177-203;
9. (b) Aim, E.; Baker, D. Curr Opin Struct Biol 1999, 9, 189-196.
10. Mirny, L.; Shakhnovich, E. I. J Mol Biol 1998, 283, 507-526.
11. (a) Skolnick, J.; Kolinski, A.; Ortiz, A. R. J Mol Biol 1997, 265, 217-241;
12. (b) Koretke, K. K.; Luthey-Schulten, Z.; Wolynes, P. G. Proc Natl Acad Sci USA 1998, 95, 2932-2937.
13. (a) Pedersen, J. T.; Moult, J. J Mol Biol 1997, 269, 240-259;
14. (b) Lee, J.; Liwo, A.; Scheraga, H. A. Proc Natl Acad Sci USA 1999, 96, 2025-2030.
15. Koehl, P.; Levitt, M. Nature Struct Biol 1999, 6, 108-111.
16. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
17. (a) Schaefer, M.; Bartels, C.; Karplus, M. J Mol Biol 1998, 284, 835-848;
18. (b) Hansmann, U. H. E.; Okamoto, Y. Curr Opin Struct Biol 1999, 9, 177-183.
19. Hoffmann, D.; Knapp, E.-W. J Phys Chem B 1997, 101, 6734-6740.
20. Ishikawa, K.; Yue, K.; Dill, K. A. Prot Sci 1999, 8, 716-721.
21. Derreumaux, P. J Chem Phys 1998, 109, 1567-1574.
22. Derreumaux, P. J Chem Phys 1999, 111, 2301-2310.
23. Metropolis, N. S., et al., J Chem Phys 1953, 21, 1087-1092.
24. Kuroda, Y.; Nakai, T.; Ohkubo, T. J Mol Biol 1994, 236, 862-868.
25. Fezoui, Y.; Connolly, P. J.; Osterhout, J. J. Prot Sci 1997, 6, 1869-1877.
26. Starovaski, M. A.; Braisted, A. C.; Wells, J. A. Proc Natl Acad Sci USA 1997, 94, 10080-10085.
27. Deleage, G.; Blanchet, C.; Geourjon, C. Biochimie 1997, 79, 681-686.
28. Fezoui, Y.; Braswell, E. H.; Xian, W.; Osterhout, J. J. Biochemistry 1999, 38, 2796-2804.
29. Lacroix, E.; Viguera, A. R.; Serrano, L. J Mol Biol 1998, 284, 173-191.
30. De Alba, E.; Santoro, J.; Rico, M.; Jimenez, M. A. Prot Sci 1999, 8, 854-865.
31. Kalia, Y. N., et al., J Mol Biol 1993, 230, 323-341.
32. DeWitte, R. S.; Shakhnovich, E. I. Prot Sci 1994, 3, 1570-1581.