Computational studies of RNA and DNA

Basics of Nucleic Acid Structure:Concepts, Tools, and Archives.- Using Amber to simulate DNA and RNA.- Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes Using CHARMM.- Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes With Ligands.- Data Mining of Molecular Dynamic Trajectories of Nucleic Acids.- Enhanced Sampling Methods for Atomistic Simulation Of Nucleic Acids.- Modeling DNA Deformation.- Molecular Dynamics Simulations and Free Energy Calculations on Protein-Nucleic Acid Complexes.- DNA Simulation Benchmarks as Revealed by X-Ray Structures.-RNA: The Cousin Left Behind Becomes a Star.- Molecular dynamics simulations of RNA systems: importance of the initial conditions- RNA molecular dynamics.- Molecular dynamics simulations of nucleic acids: MD simulations of G-DNA and functional RNAs.- Using Computer Simulations to Study Decoding by the Ribosome.- Base stacking and base pairing: Advanced quantum chemical studies.- Interaction of Metal Cations With Nucleic Acids and their Building Units: A comprehensive view from quantum chemical calculations.- Proton transfer in DNA base pairs: Potential mutagenic processes.- Comparative Study of Quantum Mechanical Methods Related to Nucleic Acid Bases: Electronic Spectra, Excited State Structures and Interactions.- Substituent Effects on Hydrogen Bonds in DNA:A Kohn-Sham DFT approach.- Computational modeling of charge transfer in DNA.- Quantum chemical calculations of NMR parameters.- The Importance of Entropic Factors In DNA Behaviour: Insights From Simulations.- Sequence-dependent harmonic deformability of nucleic acids inferred from atomistic molecular dynamics.- Simulation of equilibrium and dynamic properties of large DNA molecules.- Chromatin Simulations: From DNA to chromatin fibers.