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Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites

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Computational Methods for Macromolecules: Challenges and Applications

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 24))

Abstract

Recent methodological developments led to longer and more accurate molecular dynamics (MD) simulations. In parallel, methods have been designed with the purpose of characterizing water and ion binding features. Here, we give an outline of some of the methods we used in order to extract structural and dynamical information concerning the first water and ion coordination shell, from MD simulations conducted on RNA and DNA structures. Coordinates for the water and ion binding sites located in the first coordination shell of r(G=C), d(G=C), r(A-U), and d(A-T) base-pairs are provided, along with calculated “pseudo” thermal factors.

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Author information

Authors and Affiliations

  1. Institut de Biologie Moléculaire et Cellulaire du CNRS Modélisations et Simulations des Acides Nucléiques, UPR 9002 15 rue René Descartes, F-67084, Strasbourg Cedex, France

    Pascal Auffinger, Benoit Masquida & Eric Westhof

Authors
  1. Pascal Auffinger
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  2. Benoit Masquida
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  3. Eric Westhof
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Editor information

Editors and Affiliations

  1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

  2. Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

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© 2002 Springer-Verlag Berlin Heidelberg

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Auffinger, P., Masquida, B., Westhof, E. (2002). Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites. In: Schlick, T., Gan, H.H. (eds) Computational Methods for Macromolecules: Challenges and Applications. Lecture Notes in Computational Science and Engineering, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56080-4_3

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  • DOI: https://doi.org/10.1007/978-3-642-56080-4_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43756-7

  • Online ISBN: 978-3-642-56080-4

  • eBook Packages: Springer Book Archive

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