Computational Studies of RNA and DNA
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 calcul
- PDF / 24,954,247 Bytes
- 638 Pages / 325.984 x 502.181 pts Page_size
- 0 Downloads / 188 Views
CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS Volume 2
Series Editor:
JERZY LESCZYNSKI Department of Chemistry, Jackson State University, U.S.A.
Computational Studies of RNA and DNA Edited by
J. Šponer Institute of Biophysics, Academy of Sciences of the Czech Republic
and
F. Lankaš Institute for Mathematics B, EPFL (Swiss Federal Institute of Technology), Lausanne, Switzerland
A C.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN-10 ISBN-13 ISBN-10 ISBN-13
1-4020-4794-0 (HB) 978-1-4020-4794-7 (HB) 1-4020-4851-3 (e-book) 978-1-4020-4851-3 (e-book)
Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. www.springer.com
Printed on acid-free paper
All Rights Reserved © 2006 Springer No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.
CONTENTS
Preface 1.
2.
3.
4.
5.
6.
7.
8.
ix Basics of Nucleic Acid Structure Bohdan Schneider and Helen M. Berman
1
Using Amber to Simulate DNA and RNA Thomas E. Cheatham, III and David A. Case
45
Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm Alexander D. MacKerell, Jr. and Lennart Nilsson
73
Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands Martin Zacharias
95
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
121
Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids Catherine Kelso and Carlos Simmerling
147
Modeling DNA Deformation Péter Várnai and Richard Lavery
169
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
211
v
vi 9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
Contents DNA Simulation Benchmarks as Revealed by X-Ray Stru r ctu t res Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge, Guohui Zheng, and Victor B. Zhurkin
235
RNA:The Cousin Left Behind Becomes a Star Tamar Schlick
259
Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions Pascal Auffinger
283
Molecular Dynamics Simulations of Nucleic Acids Nad‘a Špaþková, þ Thomas E. Cheatham, III and JiĜí Šponer
301
Using Computer Simulations to Study Decoding by the Ribosome Kevin Y. Sanbonmatsu
327
Base Stacking and Base Pairing JiĜí Šponer, Petr Jureþka þ and Pavel Hobza
343
Interaction of Metal Cations with Nucleic Acids and their Building Units Judit E. Šponer, Jaroslav V. Burda, Jerzy Leszc
