TU Darmstadt / ULB / TUprints

StreAM-Tg : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

Jager, Sven and Schiller, Benjamin and Babel, Philipp and Blumenroth, Malte and Strufe, Thorsten and Hamacher, Kay :
StreAM-Tg : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs.
In: Algorithms for Molecular Biology, 12 (1) ISSN 1748-7188
[Article], (2017)

[img]
Preview
Text
Jager.pdf
Available under CC-BY 4.0 International - Creative Commons Attribution 4.0.

Download (2MB) | Preview
Item Type: Article
Title: StreAM-Tg : algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs
Language: English
Abstract:

Background

In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of k nucleotides. Based on those, we define transitions between states as changes in the adjacency matrices which form Markovian dynamics. The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-Tg, a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices representing the RNA.

Results

We benchmark StreAM-Tg(a) for random and RNA unit sphere dynamic graphs (b) for the robustness of our method against different parameters. Moreover, we address a riboswitch design problem by applying StreAM-Tg on six long term molecular dynamics simulation of a synthetic tetracycline dependent riboswitch (500 ns) in combination with five different antibiotics.

Conclusions

The proposed algorithm performs well on large simulated as well as real world dynamic graphs. Additionally, StreAM-Tg provides insights into nucleotide based RNA dynamics in comparison to conventional metrics like the root-mean square fluctuation. In the light of experimental data our results show important design opportunities for the riboswitch.

Journal or Publication Title: Algorithms for Molecular Biology
Volume: 12
Number: 1
Publisher: Biomed Central
Classification DDC: 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
Divisions: 10 Department of Biology > Computational Biology and Simulation
Date Deposited: 12 Sep 2017 13:38
Last Modified: 12 Sep 2017 13:38
URN: urn:nbn:de:tuda-tuprints-67942
Identification Number: 10.1186/s13015-017-0105-0
URI: http://tuprints.ulb.tu-darmstadt.de/id/eprint/6794
Export:
Actions (login required)
View Item View Item

Downloads

Downloads per month over past year