Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

Journal of Chemical Physics

Volumn 135, Issue 8, 2011, Pages

  Chevrot, Guillaume ^a,b   Calligari, Paolo ^c   Hinsen, Konrad ^a,b   Kneller, Gerald R ^a,b,d  

^a CENTRE DE BIOPHYSIQUE MOLÉCULAIRE   (France)

^b SYNCHROTRON SOLEIL   (France)

^c ECOLE NORMALE SUPÉRIEURE   (France)

^d UNIVERSITÉ D'ORLÉANS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC COORDINATE; ATOMIC DISPLACEMENT; CLASSICAL APPROACH; INPUT AND OUTPUTS; INPUT TRAJECTORY; INTERNAL ENERGIES; INTERNAL MOTION; LEAST CONSTRAINT; MOLECULAR DYNAMICS TRAJECTORIES; NUMERICAL EXAMPLE; RIGID-BODY MOTION; ROTATIONAL SUPERPOSITION; SMALL SAMPLING; TIME FRAME; TIME INCREMENTS;

ATOMS; MACROMOLECULES; MOLECULAR DYNAMICS;

TRAJECTORIES;

ARTICLE; MOLECULAR DYNAMICS; THEORETICAL MODEL;

MODELS, THEORETICAL; MOLECULAR DYNAMICS SIMULATION;

EID: 80052410200     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3626275     Document Type: Article

References (32)

1. R. Abseher, S. Ldemann, H. Schrieber, and O. Steinhauser, J. Mol. Biol. 249, 604 (1995). 10.1006/jmbi.1995.0322
2. J. Chen, C. Brooks, and P. Wright, J. Biomol. NMR 29, 243 (2004). 10.1023/B:JNMR.0000032504.70912.58
3. A. Nederveen and A. Bonvin, J. Chem. Theory Comput. 1, 363 (2005). 10.1021/ct0498829
4. V. Calandrini, D. Abergel, and G. R. Kneller, J. Chem. Phys. 133, 145101 (2010). 10.1063/1.3486195
5. G. Kneller and V. Calandrini, Biochim. Biophys. Acta 1804, 56 (2010). 10.1016/j.bbapap.2009.05.007
6. C. Eckart, Phys. Rev. 47, 552 (1935). 10.1103/PhysRev.47.552
7. A. Sayvetz, J. Chem. Phys. 7, 383 (1939). 10.1063/1.1750455
8. K. Kudin and A. Dymarsky, J. Chem. Phys. 122, 224105 (2005). 10.1063/1.1929739
9. C. Gauss, J. Reine Angew. Math. 4, 232 (1829). 10.1515/crll.1829.4.232
10. G. Kneller, J. Chem. Phys. 128, 194101 (2008). 10.1063/1.2902290
11. L. Pars, A Treatise on Analytical Dynamics (Heinemann, London, 1965).
12. C. Lanczos, The variational Principles of Mechanics, 4th ed. (University of Toronto, Toronto, 1974).
13. G. Kneller, J. Chem. Phys. 127, 164114 (2007). 10.1063/1.2779326
14. S. Altmann, Rotations, Quaternions, and Double Groups (Clarendon, Oxford, 1986).
15. R. Diamond, Acta Crystallogr. A 44, 211 (1988). 10.1107/S0108767387010535
16. R. Diamond, Acta Crystallogr. A 46, 423 (1990). 10.1107/S0108767390002239
17. G. Kneller, Mol. Simul. 7, 113 (1991). 10.1080/08927029108022453
18. D. Flower, J. Mol. Graph. Model. 17, 238 (1999). 10.1016/S1093-3263(00) 00033-4
19. G. Kneller and P. Calligari, Acta Crystallogr. D 62, 302 (2006). 10.1107/S0907444905042654
20. B. Barua, J. C. Lin, V. D. Williams, P. Kummler, J. W. Neidigh, and N. H. Andersen, Protein Eng. Des. Sel. 21, 171 (2008). 10.1093/protein/gzm082
21. J. Kirchmair, P. Markt, S. Distinto, D. Schuster, G. M. Spitzer, K. R. Liedl, T. Langer, and G. Wolber, J. Med. Chem. 51, 7021 (2008). 10.1021/jm8005977
22. K. Hinsen, J. Comput. Chem. 21, 79 (2000); see URL http://dirac.cnrs- orleans.fr. 10.1002/(SICI)1096-987X(20000130)21:279::AID-JCC13.0.CO;2-B
23. J. Wang, P. Cieplak, and P. Kollman, J. Comput. Chem. 21, 1049 (2000). 10.1002/1096-987X(200009)21:121049::AID-JCC33.0.CO;2-F
24. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
25. D. Wolf, P. Keblinski, S. Philpot, and J. Eggebrecht, J. Chem. Phys. 110, 8254 (1999). 10.1063/1.478738
26. A. Angoshtari and A. Yavari, Phys. Lett. A 375, 1281 (2011). 10.1016/j.physleta.2011.01.048
27. D. A. C. Beck, R. S. Armen, and V. Daggett, Biochemistry 44, 609 (2005). 10.1021/bi0486381
28. S. Nosé, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
29. D. Case, T. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr. , A. Onufriev, C. Simmerling, B. Wang, and R. Woods, J. Comput. Chem. 26, 1668 (2005). 10.1002/jcc.20290
30. Y. Duan, C. Wu, S. Chowdhury, M. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, and T. Lee, J. Comput. Chem. 24, 1999 (2003). 10.1002/jcc.10349
31. G. Hawkins, C. Cramer, and D. Truhlar, Chem. Phys. Lett. 246, 122 (1995). 10.1016/0009-2614(95)01082-K
32. G. Hawkins, C. Cramer, and D. Truhlar, J. Phys. Chem. 100, 19824 (1996). 10.1021/jp961710n