title: Physics-based RNA structure prediction.
abstract: Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures' predictions and then focus on a recently developed RNA statistical mechanical model-the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions.
authors.affiliation: Department of Physics, University of Missouri, Columbia, MO 65211 USA ; Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA ; Informatics Institute, University of Missouri, Columbia, MO 65211 USA.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Physics, University of Missouri, Columbia, MO 65211 USA ; Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA ; Informatics Institute, University of Missouri, Columbia, MO 65211 USA.
authors.forename: Shi-Jie
authors.initials: SJ
authors.lastname: Chen
keywords: 2D structure prediction; 3D structure prediction; RNA; Tertiary motif; Vfold