© 2006

Computational Studies of RNA and DNA

  • J. Šponer
  • F. Lankaš

Table of contents

  1. Front Matter
    Pages i-xi
  2. Bohdan Schneider, Helen M. Berman
    Pages 1-44
  3. Thomas E. Cheatham III, David A. Case
    Pages 45-71
  4. Alexander D. MacKerell Jr., Lennart Nilsson
    Pages 73-94
  5. Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda, Carles Ferrer, Antonio Valencia et al.
    Pages 121-145
  6. Catherine Kelso, Carlos Simmerling
    Pages 147-167
  7. Péter Várnai, Richard Lavery
    Pages 169-210
  8. David L. Beveridge, Surjit B. Dixit, Bethany L. Kormos, Anne M. Baranger, B. Jayaram
    Pages 211-234
  9. Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge, Guohui Zheng, Victor B. Zhurkin
    Pages 235-257
  10. Tamar Schlick
    Pages 259-281
  11. Nad'a Špačková, Thomas E. Cheatham III, Jiří Šponer
    Pages 301-325
  12. Jiří Šponer, Petr Jurečka, Pavel Hobza
    Pages 343-388
  13. Judit E. Šponer, Jaroslav V. Burda, Jerzy Leszczynki, Jiří Šponer
    Pages 389-410
  14. J. Bertran, L. Blancafort, M. Noguera, M. Sodupe
    Pages 411-432
  15. Célia Fonseca Guerra, F. Matthias Bickelhaupt
    Pages 463-484
  16. Alexander A. Voityuk
    Pages 485-511

About this book


Computational Studies of RNA and DNA

Jiri Sponer and Filip Lankas


Computational Studies of RNA and DNA includes, in an integrated way, modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.

The systems and problems studied include:

  • Accurate calculations of base pairing energies
  • Electronic properties of nucleic acids and electron transfer, through various types of nucleic acid
  • Calculating DNA elasticity

This book is ideally suited to academics and researchers in organic and computational chemistry as well as biochemistry and particularly those interested in the molecular modelling of nucleic acids.

Besides the state-of-the art science, the book also provides introductory information to non-specialists to enter and understand this field.


Base Computational Chemistry DNA DNA and RNA mechanics DNA and RNA structure and dynamics Mesoscopic Modelling Molecular Dynamics Molecular Modelling RNA biochemistry

Editors and affiliations

  • J. Šponer
    • 1
  • F. Lankaš
    • 2
  1. 1.Institute of BiophysicsAcademy of SciencesCzech Republic
  2. 2.Institute for Mathematics BEPFL (Swiss Federal Institute of Technology)LausanneSwitzerland

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