Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure

Abstract

This paper describes a new all-atom Monte Carlo (MC) simulation program for RNAs. The core numerical engine of this program is powered exclusively by inverse kinematic loop closures. The new simulation program called Loops MC is aimed at the high-efficiency sampling of large-scale conformational rearrangements in long-chain biomolecules including nucleic acids and proteins. The program and its source codes are available at http://tyrosine.usc.edu. The details of the loop closure algorithm and how it is implemented in Loops MC, as well as the various features of the program are discussed in this paper. Results of a large-scale unfolding study of the Schistosoma hammerhead ribozyme using Loops MC and their implications on the hammerhead's possible folding pathway are reported here.

Keywords:

• biomolecular simulation programs
• RNA conformational sampling
• loop closure
• Monte Carlo simulations of RNAs
• RNA folding and unfolding

Acknowledgements

This material is based upon work supported by the National Science Foundation under CHE-0713981.