Determining geometrically stable domains in molecular conformation sets

Journal of Chemical Theory and Computation

Volumn 8, Issue 8, 2012, Pages 2588-2599

  Romanowska, Julia ^a,b   Nowiński, Krzysztof S ^b   Trylska, Joanna ^c  

^a UNIVERSITY OF WARSAW   (Poland)

^b UNIVERSITY OF WARSAW   (Poland)

^c UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84865093095     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300206j     Document Type: Article

References (57)

1. Karplus, M.; Kuriyan, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6679-6685
2. Henzler-Wildman, K.; Kern, D. Nature 2007, 450, 964-972
3. Karplus, M.; McCammon, J. A. Nat. Struct. Biol. 2002, 9, 646-652
4. Leach, A. R. Molecular Modelling: Principles and Applications; Pearson Education/Prentice Hall: Englewood Cliffs, NJ, 2001.
5. Schlick, T. In Molecular Modeling and Simulation. An Interdisciplinary Guide, 1 st ed.; Marseden, J.; Sirovich, L.; Wiggins, S.; Antman, S., Eds.; Springer: New York, 2006.
6. Romanowska, J.; Setny, P.; Trylska, J. J. Phys. Chem. B 2008, 112, 15227-15243
7. Grant, B. J.; Gorfe, A. A.; McCammon, J. A. Curr. Opin. Struct. Biol. 2010, 20, 142-147
8. Vásquez, V.; Sotomayor, M.; Cordero-Morales, J.; Schulten, K.; Perozo, E. Science 2008, 321, 1210-1214
9. Skjaerven, L.; Grant, B. J.; Muga, A.; Teigen, K.; McCammon, J. A.; Reuter, N.; Martinez, A. PLoS Comput. Biol. 2011, 7, e1002004
10. Jensen, M. O.; Tajkhorshid, E.; Schulten, K. Structure 2001, 9, 1083-1093
11. Rao, F.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 9152-9157
12. Sorin, E. J.; Pande, V. S. Biophys. J. 2005, 88, 2472-2493
13. Andrec, M.; Felts, A. K.; Gallicchio, E.; Levy, R. M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6801-6806
14. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science 2011, 334, 517-520
15. Klenin, K.; Strodel, B.; Wales, D. J.; Wenzel, W. Biochim. Biophys. Acta 2011, 1814, 977-1000
16. Christen, M.; van Gunsteren, W. F. J. Computat. Chem. 2008, 29, 157-166
17. Zwier, M. C.; Chong, L. T. Curr. Opin. Pharmacol. 2010, 10, 745-752
18. Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. J. Chem. Theory Comput. 2007, 3, 2312-2334
19. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Proteins: Struct., Funct., Bioinf. 1993, 17, 412-425
20. Wriggers, W.; Schulten, K. Proteins: Struct., Funct., Bioinf. 1997, 29, 1-14
21. Hinsen, K. Proteins: Struct., Funct., Bioinf. 1998, 33, 417-429
22. Hinsen, K.; Thomas, A.; Field, M. J. Proteins: Struct., Funct., Bioinf. 1999, 34, 369-382
23. Snyder, D. A.; Montelione, G. T. Proteins: Struct., Funct., Bioinf. 2005, 59, 673-686
24. Qi, G.; Lee, R.; Hayward, S. Bioinformatics 2005, 21, 2832-2838
25. Poornam, G. P.; Matsumoto, A.; Ishida, H.; Hayward, S. Proteins: Struct., Funct., Bioinf. 2009, 76, 201-212
26. Grant, B. J.; Rodrigues, A. P. C.; ElSawy, K. M.; McCammon, J. A.; Caves, L. S. D. Bioinformatics 2006, 22, 2695-2696
27. Aleksiev, T.; Potestio, R.; Pontiggia, F.; Cozzini, S.; Micheletti, C. Bioinformatics 2009, 25, 2743-2744
28. Kirchner, D. K.; Guntert, P. BMC Bioinformatics 2011, 12, 170-181
29. Roccatano, D.; Mark, a. E.; Hayward, S. J. Mol. Biol. 2001, 310, 1039-1053
30. Tozzini, V.; Trylska, J.; Chang, C.; Mccammon, J. A. J. Struct. Biol. 2007, 157, 606-615
31. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38
32. Hayward, S. In Computational Biochemistry and Biophysics, 1 st ed.; Becker, O. M.; MacKerell; Alexander, D. J.; Roux, B.; Watanabe, M., Eds.; Taylor & Francis: New York, 2001; pp 153-168.
33. Potestio, R.; Pontiggia, F.; Micheletti, C. Biophys. J. 2009, 96, 4993-5002
34. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242
35. Hamilton, S. W. R. Elements of Quaternions (Google eBook); Longmans, Green, & Co., 1866.
36. Kuipers, J. B. Quaternions and Rotation Sequences: A Primer with Applications to Orbits, Aerospace, and Virtual Reality; Princeton University Press: Princeton, NJ, 2002.
37. Kneller, G. R.; Calligari, P. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2006, 62, 302-311
38. Keller, B.; Daura, X.; van Gunsteren, W. F. J. Chem. Phys. 2010, 132, 074110-074116
39. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
40. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, 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, 1545-1614
41. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 564-578
42. Campos-Olivas, R.; Newman, J. L.; Summers, M. F. J. Mol. Biol. 2000, 296, 633-649
43. Lukavsky, P. J.; Kim, I.; Otto, G. A.; Puglisi, J. D. Nat. Struct. Biol. 2003, 10, 1033-1038
44. Ramos, A.; Grünert, S.; Adams, J.; Micklem, D. R.; Proctor, M. R.; Freund, S.; Bycroft, M.; St. Johnston, D.; Varani, G. EMBO J. 2000, 19, 997-1009
45. Kulczycka, K.; Døugosz, M.; Trylska, J. Eur. Biophys. J. 2011, 40, 289-303
46. Skjaerven, L.; Muga, A.; Reuter, N.; Martinez, A. Proteins: Struct., Funct., Bioinf. 2012, in press.
47. Horwich, A. L.; Fenton, W. A. Q. Rev. Biophys. 2009, 42, 83-116
48. Xu, Z.; Horwich, A. L.; Sigler, P. B. Nature 1997, 388, 741-750
49. Ma, J.; Sigler, P. B.; Xu, Z.; Karplus, M. J. Mol. Biol. 2000, 302, 303-313
50. de Groot, B. L.; Vriend, G.; Berendsen, H. J. J. Mol. Biol. 1999, 286, 1241-1249
51. Nissen, P.; Kjeldgaard, M.; Thirup, S.; Polekhina, G.; Reshetnikova, L.; Clark, B. F.; Nyborg, J. Science 1995, 270, 1464-1472
52. Abel, K.; Yoder, M. D.; Hilgenfeld, R.; Jurnak, F. Structure 1996, 4, 1153-1159
53. Polekhina, G.; Thirup, S.; Kjeldgaard, M.; Nissen, P.; Lippmann, C.; Nyborg, J. Structure 1996, 4, 1141-1151
54. Réblová, K.; Rázga, F.; Li, W.; Gao, H.; Frank, J.; Šponer, J. Nucleic Acids Res. 2010, 38, 1325-1340
55. Laurberg, M.; Kristensen, O.; Martemyanov, K.; Gudkov, A. T.; Nagaev, I.; Hughes, D.; Liljas, A. J. Mol. Biol. 2000, 303, 593-603
56. Rázga, F.; Zacharias, M.; Réblová, K.; Koča, J.; Šponer, J. Structure 2006, 14, 825-835
57. R Development Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2011, (ISBN 3-900051-07-0).