A local rigid body framework for global optimization of biomolecules

Journal of Chemical Theory and Computation

Volumn 8, Issue 12, 2012, Pages 5159-5165

  Kusumaatmaja, Halim ^a   Whittleston, Chris S ^a   Wales, David J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84870916588     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct3004589     Document Type: Conference Paper

References (40)

1. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141
2. Wang, F.; Landau, D. P. Phys. Rev. Lett. 2001, 86, 2050
3. Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187
4. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562
5. Gohlke, H.; Thorpe, M. F. Biophys. J. 2006, 91, 2115
6. Zhang, Z.; Lu, L.; Noid, W. G.; Krishna, V.; Pfaendtner, J.; Voth, G. A. Biophys. J. 2008, 95, 5073
7. Monticelli, L.; Kandasamy, S. K.; Periole, X.; Larson, R. G.; Tieleman, D. P.; Marrink, S.-J. J. Chem. Theory Comput. 2008, 4, 819
8. Heath, A. P.; Kavraki, L. E.; Clementi, C. Proteins: Struct., Funct., Bioinf. 2007, 68, 646
9. Sherwood, P.; Brooks, B. R.; Sansom, M. S. P. Curr. Opin. Struct. Biol. 2008, 18, 630
10. Noid, W. G.; Chu, J. W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. J. Chem. Phys. 2008, 128, 244114
11. Dupuis, L.; Mousseau, N. J. Chem. Phys. 2012, 136, 035101
12. Dupuis, L.; Mousseau, N. J. Phys.: Conf. Ser. 2012, 341, 012015
13. Wales, D. J. Energy Landscapes; Cambridge University Press: Cambridge, U. K., 2003; p 340-346.
14. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611
15. Wales, D. J.; Doye, J. P. K. J. Phys. Chem. A 1997, 101, 5111
16. Wales, D. J.; Scheraga, H. A. Science 1999, 285, 1368
17. Kitao, A.; Go, N. Curr. Opin. Struct. Biol. 1999, 9, 164
18. Balsera, M. A.; Wriggers, W.; Oono, Y.; Schulten, K. J. Chem. Phys. 1996, 100, 2567
19. Jacobs, D. J.; Thorpe, M. F. Phys. Rev. Lett. 1995, 75, 4051
20. Cochran, A. G.; Skelton, N. J.; Starovasnik, M. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 5578
21. Honda, S.; Yamasaki, K.; Sawada, Y.; Morii, H. Structure 2004, 12, 1507
22. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Caflisch, S. B. A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1615
23. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217
24. Ponder, J. W.; Case, D. A. Adv. Protein Chem. 2003, 66, 27-85
25. Case, D.; Darden, T.; Cheatham, T., III; Simmerling, C.; Wang, J.; Duke, R.; Luo, R.; Walker, R.; Zhang, W.; Merz, K.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A.; Kolossvai, I.; Wong, K.; Paesani, F.; Vanicek, J.; Wolf, R.; Liu, J.; Wu, X.; Brozell, S.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D.; Mathews, D.; Seetin, M.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. Amber 12; University of California: San Francisco, CA, 2012.
26. Wales, D. J. GMIN: A program for finding global minima and calculating thermodynamic properties. http://www-wales.ch.cam.ac.uk/GMIN (accessed August 1, 2012).
27. Yun, M.-R.; Lavery, R.; Mousseau, N.; Zakrzewska, K.; Derreumaux, P. Proteins: Struct., Funct., Bioinf. 2006, 63, 967
28. Mortensen, P. N.; Wales, D. J. J. Chem. Phys. 2001, 114, 6443
29. Whittleston, C. Ph.D. Thesis; University of Cambridge, Cambridge, U. K., 2011; pp 31-34.
30. Nocedal, J. Math. Comput. 1980, 35, 773
31. Liu, D.; Nocedal, J. Math. Program. 1989, 45, 503
32. Chakrabarti, D.; Wales, D. J. Phys. Chem. Chem. Phys. 2009, 11, 1970
33. Wales, D. J. Philos. Trans. R. Soc. London, Ser. A 2005, 363, 357
34. Brannon, R. M. Rotation. http://www.mech.utah.edu/brannon/gobag.html (accessed August 1, 2012).
35. Lazaridis, T.; Karplus, M. Proteins 1999, 35, 133
36. MaÅolepsza, E.; Strodel, B.; Khalili, M.; Trygubenko, S.; Fejer, S.; Wales, D. J. Comput. Chem. 2010, 131, 1402
37. Roy, S.; Goedecker, S.; Field, M. J.; Penev, E. J. Phys. Chem. B 1997, 101, 5111
38. Onufriev, A.; Bashford, D.; Case, D. J. Phys. Chem. B 2000, 104, 3712
39. Gibbons, J. D. Nonparametric Statistical Inference; Marcel Dekker: New York, 1985; p 483-488.
40. Tozzini, V. Curr. Opin. Struct. Biol. 2005, 15, 144