Network Theory Tools for RNA Modeling

Overview

Journal WSEAS Trans Math

Date 2014 Nov 22

PMID 25414570

Citations 18

Authors

Namhee Kim

Louis Petingi

Tamar Schlick

Affiliations

Soon will be listed here.

Abstract

An introduction into the usage of graph or network theory tools for the study of RNA molecules is presented. By using vertices and edges to define RNA secondary structures as tree and dual graphs, we can enumerate, predict, and design RNA topologies. Graph connectivity and associated Laplacian eigenvalues relate to biological properties of RNA and help understand RNA motifs as well as build, by computational design, various RNA target structures. Importantly, graph theoretical representations of RNAs reduce drastically the conformational space size and therefore simplify modeling and prediction tasks. Ongoing challenges remain regarding general RNA design, representation of RNA pseudoknots, and tertiary structure prediction. Thus, developments in network theory may help advance RNA biology.

Citing Articles

Prediction of pyrazinamide resistance in using structure-based machine-learning approaches.

Carter J, Walker T, Walker A, Whitfield M, Morlock G, Lynch C JAC Antimicrob Resist. 2024; 6(2):dlae037.

PMID: 38500518 PMC: 10946228. DOI: 10.1093/jacamr/dlae037.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.

Miao Z, Adamiak R, Antczak M, Boniecki M, Bujnicki J, Chen S RNA. 2020; 26(8):982-995.

PMID: 32371455 PMC: 7373991. DOI: 10.1261/rna.075341.120.

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.

Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y Nucleic Acids Res. 2019; 48(2):576-588.

PMID: 31799609 PMC: 7145511. DOI: 10.1093/nar/gkz1108.

An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.

Jain S, Saju S, Petingi L, Schlick T Methods. 2019; 162-163:74-84.

PMID: 30928508 PMC: 6612455. DOI: 10.1016/j.ymeth.2019.03.022.

Partitioning and Classification of RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions Using a Graph-Theoretical Approach.

Petingi L, Schlick T IAENG Int J Comput Sci. 2018; 44(2):241-246.

PMID: 30474081 PMC: 6250053.

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