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 considered include:
– Basic principles of nucleic acid structure and structural databases
– Introduction to key molecular modelling tools and methods
– Application of atomistic simulations to a wide variety of DNA and RNA systems
– Accurate QM calculations of base pairing, stacking and cation binding
– Charge transfer, excited states and NMR parameters
– Calculating mechanical properties of nucleic acids
– Mesoscopic simulation of DNA, chromatin modelling
This book is ideally suited to academics and researchers in organic and computational chemistry, structural molecular biology and biophysics 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 extensive introductory information for non-specialists and students to enter and understand this field.
Зміст
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.
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