A Bayesian statistics approach to multiscale coarse graining

Journal of Chemical Physics

Volumn 129, Issue 21, 2008, Pages

  Liu, Pu ^a   Shi, Qiang ^a   Dauḿ III, Hal ^b   Voth, Gregory A ^a  

^a UNIVERSITY OF UTAH   (United States)

^b Department of Electrical and Computer Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; EMBEDDED SYSTEMS; FEATURE EXTRACTION; LIPID BILAYERS; METHANOL; MODELS; PATTERN RECOGNITION; SIGNAL PROCESSING;

BAYES' THEOREMS; BAYESIAN; BAYESIAN APPROACHES; BAYESIAN STATISTICS; BIOLOGICAL PHENOMENONS; CG ALGORITHMS; CG FORCE FIELDS; COARSE-GRAINING; ERROR ESTIMATIONS; EXPLICIT WATERS; FORCE FIELD PARAMETERS; FORCE INFORMATIONS; HEXAPEPTIDES; MULTISCALE; POLYALANINE PEPTIDES; SIMPLE LIQUIDS; STATISTICAL TOOLS; TEMPORAL SCALES;

BAYESIAN NETWORKS;

METHANOL; PEPTIDE; POLYALANINE; UNCLASSIFIED DRUG;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN BINDING; PROTEIN CONFORMATION;

ALGORITHMS; AMINO ACID SEQUENCE; BAYES THEOREM; METHANOL; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 57349094411     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3033218     Document Type: Article

References (34)

1. S. A. Adcock and J. A. McCammon, Chem. Rev. (Washington, D.C.) 0009-2665 10.1021/cr040426m 106, 1589 (2006); M. Karplus and J. A. McCammon, Nat. Struct. Biol. 1072-8368 10.1038/nsb0902-646 9, 646 (2002); M. L. Klein and W. Shinoda, Science 0036-8075 10.1126/science.1157834 321, 798 (2008).
2. G. S. Ayton, W. G. Noid, and G. A. Voth, Curr. Opin. Struct. Biol. 0959-440X 10.1016/j.sbi.2007.03.004 17, 192 (2007); S. O. Nielsen, C. F. Lopez, G. Srinivas, and M. L. Klein, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/16/15/R03 16, R481 (2004); V. Tozzini, Curr. Opin. Struct. Biol. 0959-440X 10.1016/j.sbi.2005.02.005 15, 144 (2005); G. A. Voth, Coarse-Graining of Condensed Phase and Biomolecular Systems, 1st ed. (CRC, Boca Raton, USA, 2009).
3. S. Izvekov and G. A. Voth, J. Phys. Chem. B 1089-5647 10.1021/jp044629q 109, 2469 (2005).
4. I. F. Thorpe, J. Zhou, and G. A. Voth, J. Phys. Chem. B 112, 13079 (2008).
5. P. K. Depa and J. K. Maranas, J. Chem. Phys. 0021-9606 10.1063/1.1997150 123, 094901 (2005); C. F. Lopez, P. B. Moore, J. C. Shelley, M. Y. Shelley, and M. L. Klein, Comput. Phys. Commun. 0010-4655 10.1016/S0010-4655(02)00195-9 147, 1 (2002).
6. S. Izvekov and G. A. Voth, J. Chem. Phys. 123, (2005).
7. P. Liu, S. Izvekov, and G. A. Voth, J. Phys. Chem. B 1089-5647 10.1021/jp0721494 111, 11566 (2007).
8. W. G. Noid, J. W. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, J. Chem. Phys. 0021-9606 10.1063/1.2938860 128, 244114 (2008).
9. Y. Wang, S. Izvekov, T. Yan, and G. A. Voth, J. Phys. Chem. B 1089-5647 10.1021/jp0548220 110, 3564 (2006).
10. S. Izvekov and G. A. Voth, J. Chem. Theory Comput. 1549-9618 10.1021/ct050300c 2, 637 (2006).
11. J. Zhou, I. F. Thorpe, S. Izvekov, and G. A. Voth, Biophys. J. 0006-3495 10.1529/biophysj.106.094425 92, 4289 (2007).
12. Q. Shi, S. Izvekov, and G. A. Voth, J. Phys. Chem. B 1089-5647 10.1021/jp062700h 110, 15045 (2006).
13. W. G. Noid, P. Liu, Y. T. Wang, J. W. Chu, G. S. Ayton, S. Izvekov, H. C. Andersen, and G. A. Voth, J. Chem. Phys. 0021-9606 10.1063/1.2938857 128, 244115 (2008).
14. C. M. Bishop, Pattern Recognition and Machine Learning (Springer, New York, USA, 2006).
15. M. Habeck, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.98.200601 98, 200601 (2007).
16. S. Park, D. L. Ensign, and V. S. Pande, Phys. Rev. E 1063-651X 10.1103/PhysRevE.74.066703 74, 066703 (2006).
17. G. Hummer, New J. Phys. 1367-2630 10.1088/1367-2630/7/1/034 7, 34 (2005).
18. E. Gallicchio, M. Andrec, A. K. Felts, and R. M. Levy, J. Phys. Chem. B 1089-5647 10.1021/jp045294f 109, 6722 (2005).
19. Y. Li, J. Chem. Inf. Model. 46, 1742 (2006). 1549-9596
20. W. Rieping, M. Habeck, and M. Nilges, Science 0036-8075 10.1126/science.1110428 309, 303 (2005).
21. R. W. W. Hooft, L. H. Straver, and A. L. Spek, J. Appl. Crystallogr. 41, 96 (2008). 0021-8898
22. G. Krilov, E. Sim, and B. J. Berne, Chem. Phys. 0301-0104 10.1016/S0301-0104(01)00287-7 268, 21 (2001).
23. S. C. Kou, X. S. Xie, and J. S. Liu, Appl. Stat. 54, 469 (2005). 0035-9254
24. J. Hartigan, Ann. Math. Stat. 35, 836 (1964). 0003-4851
25. W. L. Jorgensen, J. D. Madura, and C. J. Swenson, J. Am. Chem. Soc. 0002-7863 10.1021/ja00334a030 106, 6638 (1984); W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 0002-7863 10.1021/ja9621760 118, 11225 (1996).
26. S. Nose, Mol. Phys. 0026-8976 10.1080/00268978400101201 52, 255 (1984); W. G. Hoover, Phys. Rev. A 1050-2947 10.1103/PhysRevA.31.1695 31, 1695 (1985).
27. S. W. de Leeuw, J. W. Perram, and E. R. Smith, Proc. R. Soc. London, Ser. A 0950-1207 10.1098/rspa.1980.0135 373, 27 (1980).
28. T. Forester and W. Smith, DL-POLY User Manual, CCLRC Daresburg Laboratory, 1995.
29. S. Izvekov, J. M. J. Swanson, and G. A. Voth, J. Phys. Chem. B 112, 4711 (2008). 1520-6106
30. A. D. M. B. Brooks, Jr., C. L. B. L. Nilsson III, B. Roux, Y. Won, and M. Karplus, in The Encyclopedia of Computational Chemistry, edited by, P. v. R. Schleyer, (Wiley, Chichester, 1998), Vol. 1, pp. 271.
31. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 10.1063/1.445869 79, 926 (1983).
32. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 0192-8651 10.1002/jcc.20291 26, 1701 (2005).
33. H. Stern, F. Rittner, M. Pavese, E. Harder, H. Xu, B. Kim, P. Liu, and B. J. Berne, SIM: Molecular Dynamics Simulation Program, 2005.
34. R. Nelson, M. R. Sawaya, M. Balbirnie, A. Madsen, C. Riekel, R. Grothe, and D. Eisenberg, Nature (London) 0028-0836 10.1038/nature03680 435, 773 (2005).