Measuring similarity between dynamic ensembles of biomolecules

Nature Methods

Volumn 11, Issue 5, 2014, Pages 552-554

  Yang, Shan ^a   Salmon, Loïc ^a   Al Hashimi, Hashim M ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; CONFORMATION; HUMAN IMMUNODEFICIENCY VIRUS 1; IONIC STRENGTH; MOLECULAR DYNAMICS; MOLECULE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; SIMULATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HIV LONG TERMINAL REPEAT; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, THEORETICAL; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; PROBABILITY; PROGRAMMING LANGUAGES; PROTEIN CONFORMATION; RNA, VIRAL; SOFTWARE; TEMPERATURE;

EID: 84899936219     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2921     Document Type: Article

References (22)

1. Jensen, M.R. et al. Structure 17, 1169-1185 (2009).
2. Clore, G.M. & Schwieters, C.D. Biochemistry 43, 10678-10691 (2004).
3. Salmon, L., Yang, S. & Al-Hashimi, H.M. Annu. Rev. Phys. Chem. doi:10.1146/annurev-physchem-040412-110059 (16 December 2013).
4. Boehr, D.D., Nussinov, R. & Wright, P.E. Nat. Chem. Biol. 5, 789-796 (2009).
5. Wand, A.J. Curr. Opin. Struct. Biol. 23, 75-81 (2013).
6. Stelzer, A.C. et al. Nat. Chem. Biol. 7, 553-559 (2011).
7. Richardson, J.S. & Richardson, D.C. Annu. Rev. Biophys. 42, 1-28 (2013).
8. Lindorff-Larsen, K. & Ferkinghoff-Borg, J. PLoS ONE 4, e4203 (2009).
9. Fisher, C.K., Huang, A. & Stultz, C.M. J. Am. Chem. Soc. 132, 14919-14927 (2010).
10. De Simone, A., Richter, B., Salvatella, X. & Vendruscolo, M. J. Am. Chem. Soc. 131, 3810-3811 (2009).
11. Cha, S.-H. Int. J. Math. Models Methods Appl. Sci. 1, 300-307 (2007).
12. Brüschweiler, R. Curr. Opin. Struct. Biol. 13, 175-183 (2003).
13. Frank, A.T., Stelzer, A.C., Al-Hashimi, H.M. & Andricioaei, I. Nucleic Acids Res. 37, 3670-3679 (2009).
14. Marsh, J.A., Teichmann, S.A. & Forman-Kay, J.D. Curr. Opin. Struct. Biol. 22, 643-650 (2012).
15. Chen, Y., Campbell, S.L. & Dokholyan, N.V. Biophys. J. 93, 2300-2306 (2007).
16. Tolman, J.R., Flanagan, J.M., Kennedy, M.A. & Prestegard, J.H. Proc. Natl. Acad. Sci. USA 92, 9279-9283 (1995).
17. Tjandra, N. & Bax, A. Science 278, 1111-1114 (1997).
18. Bailor, M.H., Mustoe, A.M., Brooks, C.L. III. & Al-Hashimi, H.M. Nat. Protoc. 6, 1536-1545 (2011).
19. Salmon, L., Bascom, G., Andricioaei, I. & Al-Hashimi, H.M. J. Am. Chem. Soc. 135, 5457-5466 (2013).
20. Denning, E.J., Priyakumar, U.D., Nilsson, L. & Mackerell, A.D. Jr. J. Comput. Chem. 32, 1929-1943 (2011).
21. Fisher, C.K., Zhang, Q., Stelzer, A. & Al-Hashimi, H.M. J. Phys. Chem. B 112, 16815-16822 (2008).
22. Lavery, R. & Sklenar, H. J. Biomol. Struct. Dyn. 6, 655-667 (1989).