RNA tertiary structure prediction with ModeRNA

Chapter 15 : RNA tertiary structure prediction

1 GOAL AND CHAPTER ORGANIZATION During the last decade, the number of high-quality X-ray crystallographic ribonucleic acid (RNA) three-dimensional (3-D) structures has increased significantly, and the resolution of the large ribosomal subunit crystal structure was considered a major step towards a better understanding of RNA tertiary structure and folding. The recent discovery of the RNA interf...

ModeRNA: a tool for comparative modeling of RNA 3D structure

RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, ...

On the significance of an RNA tertiary structure prediction.

Tertiary structure prediction is important for understanding structure-function relationships for RNAs whose structures are unknown and for characterizing RNA states recalcitrant to direct analysis. However, it is unknown what root-mean-square deviation (RMSD) corresponds to a statistically significant RNA tertiary structure prediction. We use discrete molecular dynamics to generate RNA-like fo...

GPU-based acceleration of an RNA tertiary structure prediction algorithm

Experimental techniques such as X-ray crystallography and nuclear magnetic resonance have been useful for the accurate determination of RNA tertiary structures. However, high-throughput structure determination using such methods often becomes difficult, due to the need for a large quantity of pure samples. Computational techniques for the prediction of RNA tertiary structures are thus becoming ...

RNA Tertiary Structure