Evaluation and optimization of discrete state models of protein folding

Journal of Physical Chemistry B

Volumn 116, Issue 37, 2012, Pages 11405-11413

  Kellogg, Elizabeth H ^a   Lange, Oliver F ^b,c   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b Munich Center for Integrated Protein Science   (Germany)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS;

CLUSTERING METHODS; CONTACT MAPS; DISCRETE STATE; DISCRETE STATE MODELS; FOLDING TRANSITION; INDIVIDUAL CONFIGURATION; INITIAL STATE; INTERPRETABILITY; K-MEANS CLUSTERING; MARKOV STATE MODELS; MOLECULAR DYNAMICS SIMULATIONS; NUMBER OF STATE; PREDICTIVE POWER; PROTEIN FOLDING SIMULATION; RESEARCH PROBLEMS; SECONDARY STRUCTURES; STATES AND TRANSITIONS; STRUCTURAL TRANSITIONS; WW DOMAIN;

PROTEIN FOLDING;

EID: 84866599221     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp3044303     Document Type: Article

References (50)

1. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y.; Wriggers, W. Science 2010, 330, 341-346
2. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science 2011, 334, 517-520
3. Chodera, J. D.; Pande, V. S. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 12969-12970
4. Rao, F.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 9152-9157
5. Ferguson, A. L.; Panagiotopoulos, A. Z.; Debenedetti, P. G.; Kevrekidis, I. G. J. Chem. Phys. 2011, 134, 135103
6. Garcia, A. E. Phys. Rev. Lett. 1992, 68, 2696-2699
7. Amadei, A.; Linssen, A. B.; Berendsen, H. J. Proteins 1993, 17, 412-425
8. Beck, D. A.; Daggett, V. Biophys. J. 2007, 93, 3382-3391
9. Best, R. B.; Hummer, G. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 1088-1093
10. Best, R. B.; Hummer, G. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6732-6737
11. Cho, S. S.; Levy, Y.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 586-591
12. Das, P.; Moll, M.; Stamati, H.; Kavraki, L. E.; Clementi, C. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 9885-9890
13. Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Trends Biochem. Sci. 2000, 25, 331-339
14. Juraszek, J.; Bolhuis, P. G. Biophys. J. 2008, 95, 4246-4257
15. Prentiss, M. C.; Wales, D. J.; Wolynes, P. G. J. Chem. Phys. 2008, 128, 225106
16. Sali, A.; Shakhnovich, E.; Karplus, M. Nature 1994, 369, 248-251
17. Weinkam, P.; Romesberg, F. E.; Wolynes, P. G. Biochemistry 2009, 48, 2394-2402
18. Stamati, H.; Clementi, C.; Kavraki, L. E. Proteins: Struct. Funct. Bioinf. 2010, 78, 223-235
19. Ferguson A., P. A.; Kevrekidis, I.; Debenedetti, P. Chem. Phys. Lett. 2011, 509, 1-11
20. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291-318
21. Huang, X.; Yao, Y.; Bowman, G. R.; Sun, J.; Guibas, L. J.; Carlsson, G.; Pande, V. S. Pac. Symp. Biocomput. 2010, 228-239
22. Bowman, G. R.; Beauchamp, K. A.; Boxer, G.; Pande, V. S. J. Chem. Phys. 2009, 131, 124101
23. Bowman, G. R.; Huang, X.; Pande, V. S. Cell Res. 2010, 20, 622-630
24. Bowman, G. R.; Pande, V. S. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 10890-10895
25. Bowman, G. R.; Voelz, V. A.; Pande, V. S. J. Am. Chem. Soc. 2011, 133, 664-667
26. Lane, T. J.; Bowman, G. R.; Beauchamp, K.; Voelz, V. A.; Pande, V. S. J. Am. Chem. Soc. 2011, 133, 18413-18419
27. Noe, F.; Schutte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 19011-19016
28. Voelz, V. A.; Bowman, G. R.; Beauchamp, K.; Pande, V. S. J. Am. Chem. Soc. 2010, 132, 1526-1528
29. Beauchamp, K. A.; Ensign, D. L.; Das, R.; Pande, V. S. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 12734-12739
30. Zhuang, W.; Cui, R. Z.; Silva, D. A.; Huang, X. J. Phys. Chem. B 2011, 115, 5415-5424
31. Buch, I.; Giorgino, T.; De Fabritiis, G. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 10184-10189
32. Noe, F.; Fischer, S. Curr. Opin. Struct. Biol. 2008, 18, 154-162
33. Pande, V. S.; Beauchamp, K.; Bowman, G. R. Methods 2010, 52, 99-105
34. Bacallado, S.; Chodera, J. D.; Pande, V. J. Chem. Phys. 2009, 131, 045106
35. Kortemme, T.; Morozov, A. V.; Baker, D. J. Mol. Biol. 2003, 326, 1239-1259
36. Rohl, C. A.; Strauss, C. E.; Misura, K. M.; Baker, D. Methods Enzymol. 2004, 383, 66-93
37. Blum, B.; Jordan, M. I.; Baker, D. Proteins: Struct., Funct., Bioinf. 2010, 78, 1583-1593
38. Lange, O. F.; Baker, D. Proteins 2012, 80, 884-895
39. Gonzalez, T. F. Theor. Comput. Sci. 1985, 38, 293-306
40. MacQueen, J. Proc.5th Berkeley Symp. Math. Statistics Probability 1967, 1, 281-297
41. Bowman, G. R.; Huang, X.; Pande, V. S. Methods 2009, 49, 197-201
42. Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. J. Chem. Phys. 2007, 126, 155101
43. Prinz, J. H.; Keller, B.; Noe, F. Phys. Chem. Chem. Phys. 2011, 13, 16912-16927
44. Prinz, J. H.; Wu, H.; Sarich, M.; Keller, B.; Senne, M.; Held, M.; Chodera, J. D.; Schutte, C.; Noe, F. J. Chem. Phys. 2011, 134, 174105
45. Beauchamp, K. A.; Bowman, G. R.; Lane, T. J.; Maibaum, L.; Haque, I. S.; Pande, V. S. J. Chem. Theory. Comput. 2011, 7, 3412-3419
46. Singhal, N.; Snow, C. D.; Pande, V. S. J. Chem. Phys. 2004, 121, 415-425
47. Berezhkovskii, A.; Hummer, G.; Szabo, A. J. Chem. Phys. 2009, 130, 205102
48. Rao, F.; Caflisch, A. J. Mol. Biol. 2004, 342, 299-306
49. Jager, M.; Nguyen, H.; Crane, J. C.; Kelly, J. W.; Gruebele, M. J. Mol. Biol. 2001, 311, 373-393
50. Deechongkit, S.; Nguyen, H.; Powers, E. T.; Dawson, P. E.; Gruebele, M.; Kelly, J. W. Nature 2004, 430, 101-105