Protein folding properties from molecular dynamics simulations

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4699 LNCS, Issue , 2007, Pages 109-115

  Van Der Spoel, David ^a   Patriksson, Alexandra ^a   Seibert, M Marvin ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MOLECULAR DYNAMICS;

CHIGNOLIN; FOLDING SIMULATIONS; TWO-STATE FOLDING REACTION;

PROTEIN FOLDING;

EID: 38049010155     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-75755-9_13     Document Type: Conference Paper

References (30)

1. Hukushima, K., Nemoto, K.: J. Phys. Soc. Jpn. 65, 1604-1608 (1996)
2. Okabe, T., Kawata, M., Okamoto, Y., Mikami, M.: Chem. Phys. Lett. 335, 435-439 (2001)
3. Okamoto, Y.: J. Molec. Graph. Model, 22, 425-439 (2004)
4. Zhou, R., Berne, B.J., Germain, R.: Proc. Natl. Acad. Sci. U.S.A. 98, 14931-14936 (2001)
5. Garcia, A.E., Onuchic, J.N.: Proc. Natl. Acad. Sci. U.S.A. 100, 13898-13903 (2003)
6. Zhou, R.: Proc. Natl. Acad. Sci. U.S.A. 100, 13280-13285 (2003)
7. Gront, D., Kolinski, A., Skolnick, J.: J. Chem. Phys. 115, 1569-1574 (2001)
8. Pitera, J.W., Swope, W.: Proc. Natl. Acad. Sci. U.S.A. 100, 7587-7592 (2003)
9. Rao, F., Caflisch, A.: J. Chem. Phys. 119(7), 4035-4042 (2003)
10. Paschek, D., Garcia, A.E.: Phys. Rev. Lett. 93, 238105 (2004)
11. Seibert, M., Patriksson, A., Hess, B., van der Spoel, D.: J. Mol. Biol. 354, 173-183 (2005)
12. Snow, C.D., Sorin, E.J., Rhee, Y.M., Pande, V.S.: Annu. Rev. Biophys. Biomol. Struct. 34, 43-69 (2005)
13. van der Spoel, D., Seibert, M.M.: Phys. Rev. Lett. 96, 238102 (2006)
14. Honda, S., Yamasaki, K., Sawada, Y., Morii, H.: Structure Fold. Des. 12, 1507-1518 (2004)
15. Jorgensen, W.L.: Encyclopedia of Computational Chemistry, vol. 3, pp. 1986-1989. Wiley, New York (1998)
16. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: J. Chem. Phys. 79, 926-935 (1983)
17. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., Haak, J.R.: J. Chem. Phys. 81, 3684-3690 (1984)
18. Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., Pedersen, L.G.: J. Chem. Phys. 103, 8577-8592 (1995)
19. Hess, B., Bekker, H., Berendsen, H.J.C., Fraaije, J.G.E.M.: J. Comp. Chem. 18, 1463-1472 (1997)
20. Miyamoto, S., Kollman, P.A.: J. Comp. Chem. 13, 952-962 (1992)
21. Berendsen, H.J.C., van der Spoel, D., van Drunen, R.: Comp. Phys. Comm. 91, 43-56 (1995)
22. Lindahl, E., Hess, B.A., van der Spoel, D.: J. Mol. Mod. 7, 306-317 (2001)
23. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., Berendsen, H.J.C.: J. Comp. Chem. 26, 1701-1718 (2005)
24. Nelder, J.A., Mead, R.: Computer J. 7, 308-315 (1965)
25. Luzar, A., Chandler, D.: Nature 379, 55-57 (1996)
26. Luzar, A.: J. Chem. Phys. 113, 10663-10675 (2000)
27. van der Spoel, D., van Maaren, P.J., Larsson, P., Timneanu, N.: J. Phys. Chem. B 110, 4393-4398 (2006)
28. Shirts, M.R., Pande, V.S.: Phys. Rev. Lett. 86, 4983-4986 (2001)
29. Snow, C.D., Nguyen, H., Pande, V.S., Gruebele, M.: Nature 420, 102-106 (2002)
30. Rhee, Y.M., Sorin, E.J., Jayachandran, G., Lindahl, E., Pande, V.S.: Proc. Natl. Acad. Sci. U.S.A. 101, 6456-6461 (2004)