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Conformational Dynamics Simulations of Proteins

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Computational Molecular Dynamics: Challenges, Methods, Ideas

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 4))

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Abstract

Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales.

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Author information

Authors and Affiliations

  1. Institut für Medizinische Optik, Theoretische Biophysik, Ludwig-Maximilians-Universität München, Oettingenstraβe 67, D-80538, München, Germany

    Markus Eichinger, Berthold Heymann, Helmut Heller, Helmut Grubmüller & Paul Tavan

Authors
  1. Markus Eichinger
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  2. Berthold Heymann
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  3. Helmut Heller
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  4. Helmut Grubmüller
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  5. Paul Tavan
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Editor information

Editors and Affiliations

  1. Konrad-Zuse-Zentrum Berlin (ZIB), Takustrasse 7, D-14195, Berlin-Dahlem, Germany

    Peter Deuflhard

  2. Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599-7260, USA

    Jan Hermans

  3. Department of Mathematics, University of Kansas, 405 Snow Hall, Lawrence, KS, 66045, USA

    Benedict Leimkuhler

  4. Laboratorium für Physikalische Chemie ETH Zentrum, CH-8092, Zürich, Switzerland

    Alan E. Mark

  5. Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, GU2 5XH, UK

    Sebastian Reich

  6. Department of Computer Science, University of Illinois, 1304 West Springfield Avenue, Urbana, IL, 61801-6631, USA

    Robert D. Skeel

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© 1999 Springer-Verlag Berlin Heidelberg

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Eichinger, M., Heymann, B., Heller, H., Grubmüller, H., Tavan, P. (1999). Conformational Dynamics Simulations of Proteins. In: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A.E., Reich, S., Skeel, R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-58360-5_4

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  • DOI: https://doi.org/10.1007/978-3-642-58360-5_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63242-9

  • Online ISBN: 978-3-642-58360-5

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