Coarse-grained protein model with residue orientation energies derived from atomic force fields

Journal of Physical Chemistry B

Volumn 113, Issue 44, 2009, Pages 14824-14830

  Betancourt, Marcos R ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; LARGE SCALE SYSTEMS; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; MONTE CARLO METHODS; SIMULATORS;

ATOMIC FORCE FIELD; ATOMIC LEVELS; BOLTZMANN INVERSION; COARSE GRAINED MODELS; COARSE-GRAINED; DIHEDRAL ANGLES; HELICAL PROTEINS; NON-LOCAL INTERACTIONS; ORIENTATION DEPENDENCIES; PAIR POTENTIAL; PROTEIN MODELS; PROTEIN SIMULATIONS; PROTEIN SYSTEM; SECONDARY STRUCTURES; SIDE CHAINS; TIME-SCALES;

PROTEIN FOLDING;

EID: 72449144639     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp906710c     Document Type: Article

References (38)

1. Snow, C. D.; Nguyen, H.; Pande, V. S.; Grueble, M. Nature 2002, 420, 102-106.
2. Dill, K. A.; Ozkan, S. B.; Shell, M. S.; Weikl, T. R. Annu. Rev. Biophys. 2008, 37, 289-316.
3. Meinke, J. H.; Hansmann, U. H. E. J. Comput. Chem. 2009, 30, 1642-1648.
4. Levitt, M.; Warshel, A. Nature (London) 1975, 253, 694-698.
5. Levitt, M. J. Mol. Biol. 1976, 104, 59-107.
6. Liwo, A.; Oldziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 849-873.
7. Liwo, A.; Oldziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 874-887.
8. van Giessen, A. E.; Straub, J. E. J. Chem. Theory Comput. 2006, 2, 674-684.
9. Bereau, T.; Deserno, J. J. Chem. Phys. 2009, 130, 23510/6-23510/15.
10. Tanaka, S.; Scheraga, H. A. Macromolecules 1976, 9, 945-950.
11. Sippl, M. J. J. Mol. Biol. 1990, 213, 859-883.
12. Skolnick, J.; Jaroszewski, L.; Kolinski, A.; Godzik, A. Protein Sci. 1997, 6, 676-688.
13. Miyazawa, A.; Jernigan, R. L. Proteins 1999, 34, 49-68.
14. Regan, L.; Woolfson, D. N. Curr. Opin. Struct. Biol. 2008, 18, 475-476.
15. Kryshtafovych, A.; Fidelis, K.; Moult, J. Proteins 2009, doi: 10.1002/prot.22562.
16. Betancourt, M. R. Proteins 2009, 76, 72-85.
17. Basdevant, N.; Borgis, D.; Ha-Duong, T. J. Phys. Chem. B 2007, 111, 9390-9399.
18. Ayton, G. S.; Noid, W. G.; Voth, G. A. Curr. Opin. Struct. Biol. 2007, 17, 192-198.
19. Zhou, J.; Thorpe, I. F.; Izvekov, S.; Voth, G. A. Biophys. J. 2007, 92, 4289-4303.
20. Sherwood, P.; Brooks, B. R.; Sansom, M. S. P. Curr. Opin. Struct. Biol. 2008, 18, 630-640.
21. Betancourt, M. R.; Omovie, S. J. J. Chem. Phys. 2009, 130, 195103.
22. Thorpe, I. F.; Zhou, J.; Voth, G. A. J. Phys. Chem. B 2008, 112, 13079-13090.
23. Tobi, D.; Shafran, G.; Linial, N.; Elber, R. Proteins 2000, 40, 71-85.
24. Vendruscolo, M.; Domany, E. J. Chem. Phys. 1998, 109, 11101-11108.
25. Buchete, N. V.; Straub, J. E.; Thirumalai, D. J. Mol. Graph. Model. 2004, 22, 441-450.
26. Mukherjee, A.; Bhimalapuram, P.; Bagchi, B. J. Chem. Phys. 2005, 123, 014901.
27. Lu, M.; Dousis, A. D.; Ma, J. J. Mol. Biol. 2008, 376, 288-301.
28. Yang, Y.; Zhou, Y. Proteins 2008, 72, 793-803.
29. Fang, Q.; Shortle, D. Proteins 2005, 60, 90-96.
30. Jang, S.; Kim, E.; Pak, Y. Proteins 2007, 66, 53-60.
31. Dunbrack, R. L., Jr; Cohen, F. E. Protein Sci. 1997, 6, 1661-1681.
32. Betancourt, M. R. Submitted.
33. Betancourt, M. R. J. Phys. Chem. B 2008, 112, 5058-5069.
34. McGaughey, G. B.; Gagné, M.; Rappé, A. K. J. Biol Chem. 1998, 273, 15458-15463.
35. Meyer, E. A.; Castellano, R. K.; Diederich, F. Angew. Chem., Int. Ed. 2003, 42, 1210-1250.
36. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
37. Kim, S. Y.; Lee, J.; Lee, J. Biophys. Chem. 2005, 115, 195-200.
38. Wei, Y.; Nadler, W.; Hansmann, U. H. E. J. Chem. Phys. 2008, 128, 025105.