I will review selected aspects of modeling of folded RNAs, including recent efforts to tune the RNA AMBER force field and force field performance in microsecond-scale simulations of hairpin loops, ribozymes and riboswitches. I will discuss problems hampering accurate simulations such as overstabilization of base stacking and briefly introduce our simulation and QM/MM analysis of small ribozymes.Sponer, J. et al. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 27, 2012, 25-39.Zgarbova, M. et al. Refinement of the Cornell et al. nucleic acids force field based on reference Quantum Chemical calculations of glycosidic torsion profiles. JCTC 7, 2011, 2886-2902.Banas, P. et al. Performance of molecular mechanics force fields for RNA simulations. Stability of UUCG and GNRA hairpins. JCTC 6, 2010, 3836-3849.Mlynsky, V. et al. QM/MM Studies of Hairpin Ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. JPC B, 115, 2011, 13911-13924.

Studies of RNA molecules using explicit solvent molecular dynamics and quantum chemical calculations

245th National Meeting (2013)

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