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Modeling and Predicting RNA Three-Dimensional Structures

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1269)

Abstract

Modeling the three-dimensional structure of RNAs is a milestone toward better understanding and prediction of nucleic acids molecular functions. Physics-based approaches and molecular dynamics simulations are not tractable on large molecules with all-atom models. To address this issue, coarse-grained models of RNA three-dimensional structures have been developed. In this chapter, we describe a graphical modeling based on the Leontis–Westhof extended base-pair classification. This representation of RNA structures enables us to identify highly conserved structural motifs with complex nucleotide interactions in structure databases. Further, we show how to take advantage of this knowledge to quickly and simply predict three-dimensional structures of large RNA molecules.

Key words

Tertiary structure RNA motifs Extended secondary structure Base-pair classification Modeling Prediction 
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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.School of Computer ScienceMcGill UniversityMontrealCanada

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