Skip to main content

Normal Mode Analysis

  • Chapter
  • First Online:
Computer Simulations in Molecular Biology

Part of the book series: Scientific Computation ((SCIENTCOMP))

  • 276 Accesses

Abstract

This chapter introduces the normal mode analysis of a protein, which is associated with the energy minimisation.

The chapter aims to introduce the normal mode analysis of a protein.

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

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
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

References

  • I. Andricioaei, J.E. Straub, Finding the needle in the haystack: algorithms for conformational optimisation. Comput. Phys. 10, 449–454 (1996)

    Article  ADS  Google Scholar 

  • I. Andricioaei, J.E. Straub, Global optimisation using bad derivatives: derivative-free method for molecular energy minimisation. J. Comput. Chem. 19(13), 1445–1455 (1998)

    Article  Google Scholar 

  • B. Brooks, M. Karplus, Harmonic dynamics of protein: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. U.S.A. 80, 6571–6575 (1983)

    Article  ADS  Google Scholar 

  • B.R. Brooks, C.L. Brooks, A.D. MacKerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R.M. Venable, H.L. Woodcock, X. Wu, W. Yang, D.M. York, M. Karplus, Charmm: the bimolecular simulation program. J. Comput. Chem. 30(10), 1545–1614 (2009)

    Article  Google Scholar 

  • H. Goldstein, Classical Mechanics, 3rd edn. (Addison-Wesley, United State of America, 2002)

    MATH  Google Scholar 

  • W. Humphrey, A. Dalke, K. Schulten, VMD-visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)

    Article  Google Scholar 

  • H. Kamberaj, Molecular Dynamics Simulations in Statistical Physics: Theory and Applications (Computational Series. Springer Nature, Switzerland, 2020)

    Book  Google Scholar 

  • M. Karplus, J.A. McCammon, Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9(9), 646–652. With corrigenda in Nat. Struct. Biol. 9(10), 788 (2002)

    Google Scholar 

  • A.R. Leach, Molecular Modelling. Principles and Applications, 2nd edn. (Prentice Hall, Pearson Education Limited, Edingburgh Gate, 2001)

    Google Scholar 

  • M. Levitt, C. Sander, P.S. Stern, Protein normal-mode dynamics: trypsin inhibitor, cram bin, ribonuclease and lysozyme. J. Mol. Biol. 181, 423–447 (1985)

    Article  Google Scholar 

  • S. Lifson, A. Warshel, Consistent force field for calculations of conformations, vibrational spectra, and enthalpies of cycloalkane and \(n\)-alkane molecules. J. Chem. Phys. 49, 5116–5129 (1968)

    Article  ADS  Google Scholar 

  • A.D. MacKerell, Jr, D. Bashford, M. Bellot, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fisher, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, All-atom empirical potential for molecular modelling and dynamics studies of proteins. J. Phys. Chem. B 102(18), 3586–3616

    Google Scholar 

  • A.E. Sauer-Eriksson, G.J. Kleywegt, M. Uhlen, T.A. Jones, Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG. Structure 3, 265–278 (1995)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hiqmet Kamberaj .

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kamberaj, H. (2023). Normal Mode Analysis. In: Computer Simulations in Molecular Biology. Scientific Computation. Springer, Cham. https://doi.org/10.1007/978-3-031-34839-6_11

Download citation

Publish with us

Policies and ethics