Skip to main content
SpringerLink
Log in

Optimizations of Protein Force Fields

  • Chapter
  • First Online:
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

  • 853 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Liwo, A., Czaplewski, C., Stanislaw, O., Scheraga, H.A.: Curr. Opin. Struct. Biol. 18, 134 (2008)

    Article  Google Scholar 

  2. Scheraga, H.A.: Ann. Rev. Biophys. 40, 1 (2011)

    Article  Google Scholar 

  3. Hansmann, U.H.E., Okamoto, Y.: Curr. Opin. Struct. Biol. 9, 177 (1999)

    Article  Google Scholar 

  4. Mitsutake, A., Sugita, Y., Okamoto, Y.: Biopolymers 60, 96 (2001)

    Article  Google Scholar 

  5. Okamoto, Y.: J. Mol. Graphics Model. 22, 425 (2004)

    Article  Google Scholar 

  6. Mitsutake, A., Mori, Y., Okamoto, Y.: Biomolecular Simulations: Methods and Protocols. In: Monticelli, L., Salonen, E. (eds.), pp. 153–195. Humana Press, New York (2012)

    Google Scholar 

  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)

    Article  Google Scholar 

  8. Kollman, P.A., Dixon, R., Cornell, W., Fox, T., Chipot, C., Pohorille, A.: Computer Simulations of Biological Systems In: van Gunsteren, W.F., Weiner, P.K., Wilkinson, A.J., vol. 3, pp. 83–96, Kluwer/ESCOM, Dordrecht (1997)

    Google Scholar 

  9. Wang, J., Cieplak, P., Kollman, P.A.: J. Comput. Chem. 21, 1049 (2000)

    Article  Google Scholar 

  10. Hornak, V., Abel, A., Okur, R., Strockbine, B., Roitberg, A., Simmerling, C.: Proteins 65, 712 (2006)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Google Scholar 

  13. MacKerell Jr., A., Feig, M., Brooks III, C.: J. Comput. Chem. 25, 1400 (2004)

    Article  Google Scholar 

  14. MacKerell Jr., A., Feig, M., Brooks III, C.: J. Am. Chem. Soc. 126, 698 (2004)

    Article  Google Scholar 

  15. Jorgensen, W.L., Maxwell, D.S., Tirado-Rives, J.: J. Am. Chem. Soc. 118, 11225 (1996)

    Article  Google Scholar 

  16. Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: J. Phys. Chem. B 105, 6474 (2001)

    Article  Google Scholar 

  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. Oostenbrink, C., Villa, A., Mark, A.E., van Gunsteren, W.F.: J. Comput. Chem. 25, 1656 (2004)

    Article  Google Scholar 

  19. Berendsen, H.J.C., van der Spoel, D., van Drunen, R.: Comput. Phys. Commun. 91, 43 (1995)

    Article  Google Scholar 

  20. Lindahl, E., Hess, B., van der Spoel, D.: J. Mol. Model. 7, 306 (2001)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  22. Arnautova, Y.A., Jagielska, A., Scheraga, H.A.: J. Phys. Chem. B 110, 5025 (2006)

    Article  Google Scholar 

  23. Yoda, T., Sugita, Y., Okamoto, Y.: Chem. Phys. Lett. 386, 460 (2004)

    Article  Google Scholar 

  24. Yoda, T., Sugita, Y., Okamoto, Y.: Chem. Phys. 307, 269 (2004)

    Article  Google Scholar 

  25. Sakae, Y., Okamoto, Y.: Chem. Phys. Lett. 382, 626 (2003)

    Article  Google Scholar 

  26. Sakae, Y., Okamoto, Y.: J. Theor. Comput. Chem. 3, 339 (2004)

    Article  Google Scholar 

  27. Sakae, Y., Okamoto, Y.: J. Theor. Comput. Chem. 3, 359 (2004)

    Article  Google Scholar 

  28. Simmerling, C., Strockbine, B., Roitberg, A.E.: J. Am. Chem. Soc. 124, 11258 (2002)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  30. Iwaoka, M., Tomoda, S.: J. Comput. Chem. 24, 1192 (2003)

    Article  Google Scholar 

  31. Kamiya, N., Watanabe, Y., Ono, S., Higo, J.: Chem. Phys. Lett. 401, 312 (2005)

    Article  Google Scholar 

  32. Best, R.B., Hummer, G.: J. Phys. Chem. B 113, 9004 (2009)

    Article  Google Scholar 

  33. Mittal, J., Best, R.B.: Biophys. J. 99, L26 (2010)

    Article  Google Scholar 

  34. Sakae, Y., Okamoto, Y.: J. Phys. Soc. Jpn. 75, 054802 (9 pages) (2006)

    Article  Google Scholar 

  35. Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 138 (2010)

    Article  Google Scholar 

  36. Ramachandran, G.N., Sasisekharan, V.: Adv. Protein Chem. 23, 283 (1968)

    Article  Google Scholar 

  37. Tanaka, S., Scheraga, H.A.: Macromolecules 9, 945 (1976)

    Article  Google Scholar 

  38. Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 159 (2010)

    Article  Google Scholar 

  39. Sakae, Y., Okamoto, Y.: Mol. Sim. 36, 1148 (2010)

    Article  Google Scholar 

  40. Sakae, Y., Okamoto, Y.: e-print: arXiv:1206.3909 [cond-mat.stat-mech]; submitted for publication

  41. Sakae, Y., Okamoto, Y.: Mol. Sim. (In press)

    Google Scholar 

  42. Still, W.C., Tempczyk, A., Hawley, R.C., Hendrickson, T.: J. Am. Chem. Soc. 112, 6127 (1990)

    Article  Google Scholar 

  43. Qiu, D., Shenkin, P.S., Hollinger, F.P., Still, W.C.: J. Phys. Chem. A 101, 3005 (1990)

    Article  Google Scholar 

  44. Kirkpatrick, S., Gelatt Jr., C.D., Vecchi, M.P.: Science 220, 671 (1983)

    Article  MathSciNet  Google Scholar 

  45. Kabsch, W., Sander, C.: Biopolymers 22, 2577 (1983)

    Article  Google Scholar 

  46. Sakae, Y., Okamoto, Y. (In preparation)

    Google Scholar 

  47. Honda, S., Kobayashi, N., Munekata, E.: J. Mol. Biol. 295, 269 (2000)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  49. Osterhout Jr., J.J., Baldwin, R.L., York, E.J., Stewart, J.M., Dyson, H.J., Wright, P.E.: Biochemistry 28, 7059 (1989)

    Article  Google Scholar 

  50. Blanco, F.J., Rivas, G., Serrano, L.: Nature Struct. Biol. 1, 584 (1994)

    Article  Google Scholar 

  51. Kobayashi, N., Honda, S., Yoshii, H., Uedaira, H., Munekata, E.: FEBS Lett. 366, 99 (1995)

    Article  Google Scholar 

  52. Accelrys discovery studio visualizer. Software available at http://www.accelrys.com/

    Google Scholar 

  53. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R.: J. Chem. Phys. 81, 3684 (1984)

    Article  Google Scholar 

  54. Tinker program package. Software available at http://dasher.wustl.edu/tinker/

  55. URL http://www.accelrys.com/

  56. Noguchi, T., Onizuka, K., Akiyama, Y., Saito, M.: In: Proceeding of the Fifth International Conference on Intelligent Systems for Molecular Biology, AAAI press, Menlo Park, CA (1997)

    Google Scholar 

  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. Comput. Chem. 26, 1668 (2005)

    Article  Google Scholar 

  58. Onufriev, A., Bashford, D., Case, D.A.: Proteins 55, 383 (2004)

    Article  Google Scholar 

  59. Weiser, J., Shenkin, P.S., Still, W.C.: J. Comput. Chem. 20, 217 (1999)

    Article  Google Scholar 

  60. Sugita, Y., Okamoto, Y.: Chem. Phys. Lett. 314, 141 (1999)

    Article  Google Scholar 

  61. Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: J. Comput. Phys. 23, 327 (1977)

    Article  Google Scholar 

  62. Wang, G., Jr, R.L.D.: Bioinformatics 19, 1589 (2003)

    Article  Google Scholar 

  63. Hoover, W.G.: Phys. Rev. A 31, 1695 (1985)

    Article  Google Scholar 

  64. Jorgensen, W.L., Tirado-Rives, J.: J. Am. Chem. Soc. 110, 1657 (1988)

    Article  Google Scholar 

  65. Levitt, M., Chothia, C.: Nature 261, 552 (1976)

    Article  Google Scholar 

Download references

Acknowledgements

The computations were performed on the computers at the Research Center for Computational Science, Institute for Molecular Science, Information Technology Center, Nagoya University, and Center for Computational Sciences, University of Tsukuba. This work was supported, in part, by the Grants-in-Aid for the Academic Frontier Project, “Intelligent Information Science”, for Scientific Research on Innovative Areas (“Fluctuations and Biological Functions” ), and for the Next Generation Super Computing Project, Nanoscience Program and Computational Materials Science Initiative from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.

Author information

Authors and Affiliations

  1. Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, 444-8585, Japan

    Yoshitake Sakae

  2. Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan

    Yoshitake Sakae & Yuko Okamoto

  3. Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan

    Yuko Okamoto

  4. Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, 464-8603, Japan

    Yuko Okamoto

  5. Information Technology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan

    Yuko Okamoto

Authors
  1. Yoshitake Sakae
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuko Okamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuko Okamoto .

Editor information

Editors and Affiliations

  1. Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Adam Liwo

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Sakae, Y., Okamoto, Y. (2019). Optimizations of Protein Force Fields. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_7

Download citation

Publish with us

Policies and ethics

Search

Navigation