Abstract

In this chapter we review our works on force fields for molecular simulations of protein systems.We first discuss the functional forms of the force fields and present some extensions of the conventional ones.We then present various methods for force-field parameter optimizations. Finally, some examples of our applications of these parameter optimization methods are given and they are compared with the results from the existing force fields.

Keywords

Monte Carlo Protein Data Bank Total Potential Energy Kind Permission Double Fourier Series 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Liwo, A., Czaplewski, C., Stanislaw, O., Scheraga, H.A.: Curr. Opin. Struct. Biol. 18, 134 (2008)CrossRefGoogle Scholar
  2. 2.
    Scheraga, H.A.: Ann. Rev. Biophys. 40, 1 (2011)CrossRefGoogle Scholar
  3. 3.
    Hansmann, U.H.E., Okamoto, Y.: Curr. Opin. Struct. Biol. 9, 177 (1999)CrossRefGoogle Scholar
  4. 4.
    Mitsutake, A., Sugita, Y., Okamoto, Y.: Biopolymers 60, 96 (2001)CrossRefGoogle Scholar
  5. 5.
    Okamoto, Y., Mol, J.: Graphics Modell. 22, 425 (2004)CrossRefGoogle Scholar
  6. 6.
    Mitsutake, A., Mori, Y., Okamoto, Y.: In: Monticelli, L., Salonen, E. (eds.) Biomolecular Simulations: Methods and Protocols, pp. 153–195. Humana Press, New York (2012)Google Scholar
  7. 7.
    Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Kenneth, J., Merz, M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.A.: J. Am. Chem. Soc. 117, 5179 (1995)CrossRefGoogle Scholar
  8. 8.
    Kollman, P.A., Dixon, R., Cornell, W., Fox, T., Chipot, C., Pohorille, A.: In: van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J. (eds.) Computer Simulations of Biological Systems, vol. 3, pp. 83–96. Kluwer/ESCOM, Dordrecht (1997)Google Scholar
  9. 9.
    Wang, J., Cieplak, P., Kollman, P.A.: J. Comput. Chem. 21, 1049 (2000)CrossRefGoogle Scholar
  10. 10.
    Hornak, V., Abel, A., Okur, R., Strockbine, B., Roitberg, A., Simmerling, C.: Proteins 65, 712 (2006)CrossRefGoogle Scholar
  11. 11.
    Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T.: J. Comput. Chem. 24, 1999 (2003)CrossRefGoogle Scholar
  12. 12.
    MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher III., W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M.: J. Phys. Chem. B 102, 3586 (1998)CrossRefGoogle Scholar
  13. 13.
    MacKerell Jr., A., Feig, M., Brooks III, C.: J. Comput. Chem. 25, 1400 (2004)CrossRefGoogle Scholar
  14. 14.
    MacKerell Jr., A., Feig, M., Brooks III, C.: J. Am. Chem. Soc. 126, 698 (2004)CrossRefGoogle Scholar
  15. 15.
    Jorgensen, W.L., Maxwell, D.S., Tirado-Rives, J.: J. Am. Chem. Soc. 118, 11225 (1996)CrossRefGoogle Scholar
  16. 16.
    Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: J. Phys. Chem. B 105, 6474 (2001)CrossRefGoogle Scholar
  17. 17.
    Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G.: Vdf Hochschulverlag AG an der ETH Zürich, Zürich (1996)Google Scholar
  18. 18.
    Oostenbrink, C., Villa, A., Mark, A.E., van Gunsteren, W.F.: J. Comput. Chem. 25, 1656 (2004)CrossRefGoogle Scholar
  19. 19.
    Berendsen, H.J.C., van der Spoel, D., van Drunen, R.: Comput. Phys. Commun. 91, 43 (1995)CrossRefGoogle Scholar
  20. 20.
    Lindahl, E., Hess, B., van der Spoel, D.: J. Mol. Model. 7, 306 (2001)Google Scholar
  21. 21.
    Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., Scheraga, H.A.: J. Phys. Chem. 96, 6472 (1992)CrossRefGoogle Scholar
  22. 22.
    Arnautova, Y.A., Jagielska, A., Scheraga, H.A.: J. Phys. Chem. B 110, 5025 (2006)CrossRefGoogle Scholar
  23. 23.
    Yoda, T., Sugita, Y., Okamoto, Y.: Chem. Phys. Lett. 386, 460 (2004)CrossRefGoogle Scholar
  24. 24.
    Yoda, T., Sugita, Y., Okamoto, Y.: Chem. Phys. 307, 269 (2004)CrossRefGoogle Scholar
  25. 25.
    Sakae, Y., Okamoto, Y.: Chem. Phys. Lett. 382, 626 (2003)CrossRefGoogle Scholar
  26. 26.
    Sakae, Y., Okamoto, Y.: J. Theo. Comput. Chem. 3, 339 (2004)CrossRefGoogle Scholar
  27. 27.
    Sakae, Y., Okamoto, Y.: J. Theo. Comput. Chem. 3, 359 (2004)CrossRefGoogle Scholar
  28. 28.
    Simmerling, C., Strockbine, B., Roitberg, A.E.: J. Am. Chem. Soc. 124, 11258 (2002)CrossRefGoogle Scholar
  29. 29.
    Duan, Y., Wu, C., Chowdhury, S., Lee, M.C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., Kollman, P.: J. Comput. Chem. 24, 1999 (2003)CrossRefGoogle Scholar
  30. 30.
    Iwaoka, M., Tomoda, S.: J. Comput. Chem. 24, 1192 (2003)CrossRefGoogle Scholar
  31. 31.
    Kamiya, N., Watanabe, Y., Ono, S., Higo, J.: Chem. Phys. Lett. 401, 312 (2005)CrossRefGoogle Scholar
  32. 32.
    Best, R.B., Hummer, G.: J. Phys. Chem. B 113, 9004 (2009)CrossRefGoogle Scholar
  33. 33.
    Mittal, J., Best, R.B.: Biophys. J. 99, L26 (2010)CrossRefGoogle Scholar
  34. 34.
    Sakae, Y., Okamoto, Y.: J. Phys. Soc. Jpn. 75, 054802(9 pages) (2006)CrossRefGoogle Scholar
  35. 35.
    Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 138 (2010)CrossRefGoogle Scholar
  36. 36.
    Ramachandran, G.N., Sasisekharan, V.: Adv. Protein Chem. 23, 283 (1968)CrossRefGoogle Scholar
  37. 37.
    Tanaka, S., Scheraga, H.A.: Macromol. 9, 945 (1976)CrossRefGoogle Scholar
  38. 38.
    Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 159 (2010)CrossRefGoogle Scholar
  39. 39.
    Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 1148 (2010)CrossRefGoogle Scholar
  40. 40.
    Sakae, Y., Okamoto, Y.: J. Chem. Phys. 138, 064103 (2013)Google Scholar
  41. 41.
    Sakae, Y., Okamoto, Y.: Mol. Sim. 39, 85 (2013)Google Scholar
  42. 42.
    Still, W.C., Tempczyk, A., Hawley, R.C., Hendrickson, T.: J. Am. Chem. Soc. 112, 6127 (1990)CrossRefGoogle Scholar
  43. 43.
    Qiu, D., Shenkin, P.S., Hollinger, F.P., Still, W.C.: J. Phys. Chem. A 101, 3005 (1990)CrossRefGoogle Scholar
  44. 44.
    Kirkpatrick, S., Gelatt Jr., C.D., Vecchi, M.P.: Science 220, 671 (1983)MathSciNetMATHCrossRefGoogle Scholar
  45. 45.
    Kabsch, W., Sander, C.: Biopolymers 22, 2577 (1983)CrossRefGoogle Scholar
  46. 46.
    Sakae, Y., Okamoto, Y.: In preparationGoogle Scholar
  47. 47.
    Honda, S., Kobayashi, N., Munekata, E.: J. Mol. Biol. 295, 269 (2000)CrossRefGoogle Scholar
  48. 48.
    Shoemaker, K.R., Kim, P.S., Brems, D.N., Marqusee, S., York, E.J., Chaiken, I.M., Stewart, J.M., Baldwin, R.L.: Proc. Natl. Acad. Sci. U.S.A. 82, 2349 (1985)CrossRefGoogle Scholar
  49. 49.
    Osterhout Jr., J.J., Baldwin, R.L., York, E.J., Stewart, J.M., Dyson, H.J., Wright, P.E.: Biochemistry 28, 7059 (1989)CrossRefGoogle Scholar
  50. 50.
    Blanco, F.J., Rivas, G., Serrano, L.: Nature Struct. Biol. 1, 584 (1994)CrossRefGoogle Scholar
  51. 51.
    Kobayashi, N., Honda, S., Yoshii, H., Uedaira, H., Munekata, E.: FEBS Lett. 366, 99 (1995)CrossRefGoogle Scholar
  52. 52.
    Accelrys discovery studio visualizer. Software, http://www.accelrys.com/
  53. 53.
    Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R.: J. Chem. Phys. 81, 3684 (1984)CrossRefGoogle Scholar
  54. 54.
    Tinker program package. Software, http://dasher.wustl.edu/tinker/
  55. 55.
  56. 56.
    Noguchi, T., Onizuka, K., Akiyama, Y., Saito, M.: In: Proc. of the Fifth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park (1997)Google Scholar
  57. 57.
    Case, D.A., Cheatham, T., Darden, T., Gohlke, H., Luo, R., Merz Jr., K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.: J. Computat. Chem. 26, 1668 (2005)CrossRefGoogle Scholar
  58. 58.
    Onufriev, A., Bashford, D., Case, D.A.: Proteins 55, 383 (2004)CrossRefGoogle Scholar
  59. 59.
    Weiser, J., Shenkin, P.S., Still, W.C.: J. Comput. Chem. 20, 217 (1999)CrossRefGoogle Scholar
  60. 60.
    Sugita, Y., Okamoto, Y.: Chem. Phys. Lett. 314, 141 (1999)CrossRefGoogle Scholar
  61. 61.
    Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: J. Comput. Phys. 23, 327 (1977)CrossRefGoogle Scholar
  62. 62.
    Wang, G., Dunbrack Jr., R.L.: Bioinformatics 19, 1589 (2003)CrossRefGoogle Scholar
  63. 63.
    Hoover, W.G.: Phys. Rev. A 31, 1695 (1985)CrossRefGoogle Scholar
  64. 64.
    Jorgensen, W.L., Tirado-Rives, J.: J. Am. Chem. Soc. 110, 1657 (1988)CrossRefGoogle Scholar
  65. 65.
    Levitt, M., Chothia, C.: Nature 261, 552 (1976)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Yoshitake Sakae
    • 1
    • 2
  • Yuko Okamoto
    • 2
    • 3
    • 4
    • 5
  1. 1.Department of Theoretical and Computational Molecular ScienceInstitute for Molecular ScienceOkazakiJapan
  2. 2.Department of Physics, Graduate School of ScienceNagoya UniversityNagoyaJapan
  3. 3.Structural Biology Research Center, Graduate School of ScienceNagoya UniversityNagoyaJapan
  4. 4.Center for Computational Science, Graduate School of EngineeringNagoya UniversityNagoyaJapan
  5. 5.Information Technology CenterNagoya UniversityNagoyaJapan

Personalised recommendations