Biased molecular simulations for free-energy mapping: A comparison on the KcsA channel as a test case

Journal of Chemical Theory and Computation

Volumn 4, Issue 1, 2008, Pages 173-183

  Piccinini, Enrico ^a,b   Ceccarelli, Matteo ^c   Affinito, Fabio ^a,d,e   Brunetti, Rossella ^a,d   Jacoboni, Carlo ^a,d  

^a CNR Consiglio Nazionale delle Ricerche   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c UNIVERSITY OF CAGLIARI   (Italy)

^d UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^e SISSA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 38849122815     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct7001896     Document Type: Article

References (44)

1. Roux, B.; Allen, T. W.; Bernèche, S.; Im, W. Quart. Rev. Biophys. 2004, 37, 15.
2. Allen, T. W.; Andersen, O. S.; Roux, B. Biophys. J. 2006, 90, 3447.
3. Bernèche, S.; Roux, B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 8644.
4. Mapes, E. J.; Schumaker, M. F. Bull. Math. Biol. 2006, 68, 1429.
5. Piccinini, E.; Affinito, F.; Brunetti, R.; Jacoboni, C.; Rudan, M. J. Chem. Theory Comput. 2007, 3, 248.
6. Gullingsrud, J. R.; Braun, R.; Schulten, K. J. Comput. Phys. 1999, 151, 190.
7. Roux, B. Comput. Phys. Commun. 1995, 91, 275.
8. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562.
9. Zhou, Y.; Morais-Cabral, J.; Kaufman, A.; MacKinnon, R. Nature 2001, 414, 43.
10. Bernèche, S.; Roux, B. Nature 2001, 414, 73.
11. Aqvist, J.; Luzhkov, V. Nature 2002, 404, 881.
12. Bernèche, S.; Roux, B. Biophys. J. 2002, 78, 2900.
13. Gervasio, F. L.; Parrinello, M.; Ceccarelli, M.; Klein, M. L. J. Mol. Biol. 2006, 361, 390.
14. Compoint, M.; Carloni, P.; Ramseyer, C.; Girardet, C. Biochim. Biophys. Acta 2004, 1661, 26.
15. Lindhal, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306.
16. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.
17. Procacci, P.; Paci, E.; Darden, T. A.; Marchi, M. J. Comput. Chem. 1997, 18, 1848.
18. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T. A.; Lee, H.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577.
19. Tuckerman, M. E.; Berne, B. J.; Matryna, G. J. J. Chem. Phys. 1992, 97, 1990.
20. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.
21. Kumar, S.; Bouzida, D.; Swensen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011.
22. Souaille, M.; Roux, B. Comput. Phys. Commun. 2001, 135, 40.
23. Chandler D. Statistical Fluids. In Introduction to modern statistical mechanics; Oxford University Press: Oxford, New York, 1987; pp 188-233.
24. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690.
25. Hummer, G.; Szabo, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3658.
26. Crooks, G. E. J. Stat. Phys. 1998, 90, 1481.
27. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302-1.
28. Ceccarelli, M.; Danelon, C.; Laio, A.; Parrinello, M. Biophys. J. 2004, 87, 58.
29. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. J. Phys. Chem. B 2005, 109, 6714.
30. Cvijovic, D.; Klinowski, J. Science 1995, 267, 664.
31. Huber, T.; Horda, A.E.; van Gunsteren, W. F. J. Comput.-Aided Mol. Des. 1994, 8, 695.
32. Wang, F.; Landau, D. P. Phys. Rev. Lett. 2001, 86, 2050.
33. Darve, E.; Pohorille, A. J. Chem. Phys. 2001, 108, 1964.
34. Henin, J.; Chipot, C. J. Chem. Phys. 2004, 121, 2904.
35. Bussi, G.; Gervasio, F. L.; Laio, A.; Parrinello, M. J. Am. Chem. Soc. 2006, 128, 13435.
36. Piana, S.; Laio, A. J. Phys. Chem. B 2007, 111, 4553.
37. Babin, V.; Roland, C.; Darden, T. A.; Sagui, C. J. Chem. Phys. 2006, 125, 204909.
38. Jónsson, H.; Mills, G.; Jacobsen, K. W. In Classical and Quantum Dynamics in Condensed Phase Simulations; Berne, B. J., Ciccotti G., Coker, D. F., Eds.; World Scientific: Singapore, 1998; pp 385-403.
39. Gervasio, F. L.; Laio, A.; Parrinello, M. J. Am. Chem. Soc. 2005, 127, 2600.
40. Braun-Sand, S.; Burykin, A.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 2005, 109, 583.
41. Jensen, M. Ø.; Park, S.; Tajkhorshid, E.; Schulten, K. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6731.
42. Morais-Cabral, J. H.; Zhou, Y.; MacKinnon, R. Nature 2001, 414, 37.
43. Khalili-Araghi, F.; Tajkhorshid, E.; Schulten, K. Biophys. J. 2006, 91, L72.
44. Bernèche, S.; Roux, B. Structure 2005, 13, 591.