Computational Studies of RNA and DNA

ISBN-13: 9789048171958 / Angielski / Miękka / 2010 / 638 str.

Jiri Sponer; Filip Lankas; Jir Poner

Opis

This book integrates 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.

Spis treści

1. Basics of Nucleic Acid Structure, Bohdan Schneider and Helen M. Berman

2. Using Amber to Simulate DNA and RNA, Thomas E. Cheatham, III and David A. Case

3. Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm, Alexander D. MacKerell, Jr. and Lennart Nilsson

4. Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands, Martin Zacharias

5. Data Mining of Molecular Dynamic Trajectories of Nucleic Acids, Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda, Carles Ferrer, Antonio Valencia, Alberto Pérez, Oliver Carrillo, Juan Fernandez-Recio, Xavier de la Cruz and F. Javier Luque

6. Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids, Catherine Kelso and Carlos Simmerling

7. Modeling DNA Deformation, Péter Várnai and Richard Lavery

8. Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes, David L. Beveridge, Surjit B. Dixit, Bethany L. Kormos, Anne M. Baranger and B. Jayaram

9. DNA Simulation Benchmarks as Revealed by X-Ray Structures, Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge, Guohui Zheng, and Victor B. Zhurkin

10. RNA: The Cousin Left Behind Becomes a Star, Tamar Schlick

11. Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions, Pascal Auffinger

12. Molecular Dynamics Simulations of Nucleic Acids, Nad‘a Špaþková, Thomas E. Cheatham, III and Jirí Šponer

13. Using Computer Simulations to Study Decoding by the Ribosome, Kevin Y. Sanbonmatsu

14. Base Stacking and Base Pairing, Jirí Šponer, Petr Jureþka and Pavel Hobza

15. Interaction of Metal Cations with Nucleic Acids and their Building Units, Judit E. Šponer, Jaroslav V. Burda, Jerzy Leszczynki, and Jirí Šponer

16. Proton Transfer in DNA Base Pairs, J. Bertran, L. Blancafort, M. Noguera, M. Sodupe

17. Comparative Study of Quantum Mechanical Methods Related to Nucleic Acid Bases: Electronic Spectra, Excited State Structures and Interactions, M.K. Shukla and Jerzy Leszczynski

18. Substituent Effects on Hydrogen Bonds in DNA, Célia Fonseca Guerra and F. Matthias Bickelhaupt

19. Computational modeling of Charge Transfer in DNA, Alexander A. Voityuk

20. Quantum Chemical Calculations of NMR Parameters, Wolfgang Schöfberger, Vladimír Sychrovský and Lukáš Trantírek

21. The Importance of Entropic Factors in DNA Behaviour: Insights from Simulations, Sarah A. Harris and Charles A. Laughton

22. Sequence-Dependent Harmonic Deformability of Nucleic Acids Inferred from Atomistic Molecular Dynamics, Filip Lankaš

23. Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules, Alexander Vologodskii

24. Chromatin Simulations, J. Langowski and H. Schiessel

Blurb

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.