Estimation of absolute solvent and solvation shell entropies via permutation reduction

Journal of Chemical Physics

Volumn 126, Issue 1, 2007, Pages

  Reinhard, Friedemann ^a   Grubmüller, Helmut ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL MATHEMATICS; DNA; ENTROPY; FREE ENERGY; MACROMOLECULES; PROTEINS; SOLVENTS;

LENNARD JONES GASES; MACROMOLECULAR DYNAMICS; PERMUTATION REDUCTION; SOLVATION SHELLS;

MOLECULAR DYNAMICS;

BIOPOLYMER; SOLVENT; WATER;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENTROPY; SOLUTION AND SOLUBILITY; STATISTICAL MODEL;

ALGORITHMS; BIOPOLYMERS; COMPUTER SIMULATION; ENTROPY; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; SOLUTIONS; SOLVENTS; WATER;

EID: 33846037322     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2400220     Document Type: Article

References (32)

1. K. A. Dill, Protein Sci. 8, 1166 (1999).
2. N. T. Southall, K. A. Dill, and A. D. J. Haymet, J. Phys. Chem. B 1089-5647 10.1021/jp015514e 106, 521 (2002).
3. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, and V. S. Pande, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0307898101 101, 6456 (2004).
4. C. D. Snow, N. Nguyen, V. S. Pande, and M. Gruebele, Nature 0028-0836 10.1038/nature01160 420, 102 (2002).
5. B. L. de Groot and H. Grubmüller, Science 294, 2353 (2001).
6. T. Hansson, C. Oostenbrink, and W. F. van Gunsteren, Curr. Opin. Struct. Biol. 0959-440X 10.1016/S0959-440X(02)00308-1 12, 190 (2002).
7. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 1072-8368 10.1038/nsb0902-646 9, 646 (2002).
8. J. Norberg and L. Nilsson, Q. Rev. Biophys. 0033-5835 10.1017/S0033583503003895 36, 257 (2003).
9. W. F. van Gunsteren, D. Bakowies, R. Baron, Angew. Chem., Int. Ed. 45, 4064 (2006).
10. Sterling Chemistry Laboratory, J. Chem. Phys. 0021-9606 10.1063/1.1740409 22, 1420 (1954).
11. J. G. Kirkwood, J. Chem. Phys. 0021-9606 10.1063/1.1749657 3, 300 (1935).
12. T. Rodinger and R. Pomes, Curr. Opin. Struct. Biol. 0959-440X 10.1016/j.sbi.2005.03.001 15, 164 (2005).
13. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 0001-4842 10.1021/ar010030m 35, 430 (2002).
14. W. F. van Gunsteren, X. Daura, and A. E. Mark, Helv. Chim. Acta 85, 3113 (2002).
15. C. Peter, C. Oostenbrink, A. van Dorp, and W. F. van Gunsteren, J. Chem. Phys. 0021-9606 10.1063/1.1636153 120, 2652 (2004).
16. M. Karplus and J. N. Kushick, Macromolecules 14, 325 (1981).
17. J. Schlitter, Chem. Phys. Lett. 0009-2614 10.1016/0009-2614(93)89366-P 215, 617 (1993).
18. I. Andricioaei and M. Karplus, J. Chem. Phys. 0021-9606 10.1063/1.1401821 115, 6289 (2001).
19. H. Schäfer, A. E. Mark, and W. F. van Gunsteren, J. Chem. Phys. 113, 7809 (2000).
20. W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Computer Simulations of Biomolecular Systems (ESCOM Science Publishers, Leiden, 1993).
21. M. Watanabe and W. P. Reinhardt, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.65.3301 65, 3301 (1990).
22. R. M. Levy, A. R. Srinivasan, W. K. Olson, and J. A. McCammon, Biopolymers 0006-3525 10.1002/bip.360230610 23, 1099 (1984).
23. R. Böckmann, " Molekulare Dynamik von Proteinen., " Ph.D. thesis (Cuvillier Verlag, Göttingen, 2002).
24. R. E. Burkard, Discrete Appl. Math. 123, 257 (2002).
25. R. E. Burkard and E. Cela, " Linear Assignment Problems and Extensions., " Technical Report, 1998, Bericht No. 127, SFB Optimierung und Kontrolle.
26. R. Jonker and A. Volgenant, Computing 38, 325 (1987).
27. MagicLogic, http://www.magiclogic.com/assignment.html.
28. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Biomos B.V., Zürich, Groningen, 1996).
29. H. J. C. Berendsen, J. P. M. Potsma, A. DiNola, and J. R. Haak, J. Chem. Phys. 0021-9606 10.1063/1.448118 81, 3684 (1984).
30. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001).
31. R. P. White, J. Chem. Phys. 0021-9606 10.1063/1.1625920 119, 12096 (2003).
32. F. Reinhard, J. Haas, O. Lange, and H. Grubmüller, http://www.mpibpc.mpg.de/groups/grubmueller/start/software/g_permute/.