IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2018 Mar 3

PMID 29499114

Citations 34

Authors

Dong Zhang

Shi-Jie Chen

Affiliations

Soon will be listed here.

Abstract

Coarse-grained RNA folding models promise great potential for RNA structure prediction. A key component in a coarse-grained folding model is the force field. One of the challenges in the coarse-grained force field calculation is how to treat the correlation between the different degrees of freedoms. Here, we describe a new approach (IsRNA) to extract the correlated energy functions from the known structures. Through iterative molecular dynamics simulations, we build the correlation effects into the reference states, from which we extract the energy functions. The validity of IsRNA is supported by the close agreement between the simulated Boltzmann-like probability distributions for all the structure parameters and those observed from the experimentally determined structures. The correlated energy functions derived here may provide a new tool for RNA 3D structure prediction.

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