Essential dynamics: A tool for efficient trajectory compression and management

Journal of Chemical Theory and Computation

Volumn 2, Issue 2, 2006, Pages 251-258

  Meyer, Tim ^a   Ferrer Costa, Carles ^a   Pérez, Alberto ^a   Rueda, Manuel ^a   Bidon Chanal, Axel ^b   Luque, F Javier ^b   Laughton, Charles A ^c   Orozco, Modesto ^a,d,e,f  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^d Departament de Fisiologia i Immunologia (Biologia)   (Spain)

^e BARCELONA SUPERCOMPUTING CENTER   (Spain)

^f Instituto Nacional de Bioinformatica   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33750310232     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct050285b     Document Type: Article

References (19)

1. Bishop, T. C. J. Biomol. Struct. Dyn. 2005, 22, 673-686.
2. Sanbonmatsu, K. Y.; Joseph, S.; Tung, C. S. Proc. Natl. Acad. Sci. 2005, 102, 15854-9
3. Amadei, A.; Linsen, A. B. M.; Berendsen, H. J. C. Proteins 1993, 17, 412.
4. Groot, B. I. de; Hayward, S.; van Aalten, D. M. F.; Amadei, A.; Berendsen, H. J. C. Proteins 1998, 31, 116.
5. Wlodek, S. T.; Clark, T. W.; Scott, L. R.; McCammon, J. A. J. Am. Chem. Soc. 1997, 119, 9513.
6. Orozco, M.; Pérez, A.; Noy, A.; Luque, F. J. Chem. Soc. Rev. 2003, 32, 350-364.
7. Noy, A. Meyer, T.; Rueda, M.; Ferrer, C.; Valencia, A.; Perez, A.; de la Cruz, X.; Lopez, J. M.; Luque, F. J.; Orozco, M. J. Biomol. Struct. Dyn. 2005, in press.
8. AMBER8.0 Computer Program. Case, D. A. et al. University of California, San Francisco, 1999.
9. Anderson, E.; Bai, Z.; Bischof, C.; Demmel, J.; Dongarra, J.; Du Croz, J.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Ostrouchov, S.; Sorensen, D. LAPACK Users' Guide, 2nd ed.; SIAM: Philadelphia, PA, 1995.
10. Lehoucq, R. B.; Sorensen, D. C.; Yang, C. ARPACK Users' Guide: Solution of Large Scale Eigenvalue Problems with Implicitly Restarted Arnoldi Methods; SIAM: Philadelphia, PA, 1997.
11. Morreale, A.; de la Cruz, X.; Meyer, T.; Gelpí, J. L.; Luque, F. J.; Orozco, M. Proteins 2004, 58, 101-109.
12. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 11946-11975.
13. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
14. Darden, T. A.; York, D. M.; Pedersen, L. G. J. Chem. Phys. 1993, 95, 10089-10092.
15. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
16. Phillips, J.C.; Braun, R.; Wang, W.; Cumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K. J. Comput.Chem. 2005, 26, 1781-1802.
17. Ciccotti, J. P. G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
18. Pérez, A.; Blas, J. R.; Rueda, R.; López-Bes, J. M.; de la Cruz, X.; Orozco, M. J. Chem. Theory Comput. 2005, 1, 790-800.
19. Sands, Z. A.; Laughton, C. A. J. Phys. Chem. B 2004, 108, 10113-10119.