Computational studies of RNA and DNA

<P>1. Basics of Nucleic Acid Structure, Bohdan Schneider and Helen M. Berman</P>
<P>2. Using Amber to Simulate DNA and RNA, Thomas E. Cheatham, III and David A. Case</P>
<P>3. Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm, Alexander D. MacKerell, Jr. and Lennart Nilsson</P>
<P>4. Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands, Martin Zacharias </P>
<P>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 </P>
<P>6. Enhanced Sampling Methods for Atomistic Simulation of Nucleic Acids, Catherine Kelso and Carlos Simmerling </P>
<P>7. Modeling DNA Deformation, Péter Várnai and Richard Lavery </P>
<P>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 </P>
<P>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 </P>
<P>10. RNA: The Cousin Left Behind Becomes a Star, Tamar Schlick </P>
<P>11. Molecular Dynamics Simulations of RNA Systems: Importance of the Initial Conditions, Pascal Auffinger</P>
<P>12. Molecular Dynamics Simulations of Nucleic Acids, Nad‘a Špaþková, Thomas E. Cheatham, III and Jirí Šponer</P>
<P>13. Using Computer Simulations to Study Decoding by the Ribosome, Kevin Y. Sanbonmatsu</P>
<P>14. Base Stacking and Base Pairing, Jirí Šponer, Petr Jureþka and Pavel Hobza</P>
<P>15. Interaction of Metal Cations with Nucleic Acids and their Building Units, Judit E. Šponer, Jaroslav V. Burda, Jerzy Leszczynki, and Jirí Šponer</P>
<P>16. Proton Transfer in DNA Base Pairs, J. Bertran, L. Blancafort, M. Noguera, M. Sodupe</P>
<P>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</P>
<P>18. Substituent Effects on Hydrogen Bonds in DNA, Célia Fonseca Guerra and F. Matthias Bickelhaupt</P>
<P>19. Computational modeling of Charge Transfer in DNA, Alexander A. Voityuk</P>
<P>20. Quantum Chemical Calculations of NMR Parameters, Wolfgang Schöfberger, Vladimír Sychrovský and Lukáš Trantírek</P>
<P>21. The Importance of Entropic Factors in DNA Behaviour: Insights from Simulations, Sarah A. Harris and Charles A. Laughton</P>
<P>22. Sequence-Dependent Harmonic Deformability of Nucleic Acids Inferred from Atomistic Molecular Dynamics, Filip Lankaš</P>
<P>23. Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules, Alexander Vologodskii</P>
<P>24. Chromatin Simulations, J. Langowski and H. Schiessel </P>