Graph-based sampling for approximating global helical topologies of RNA

Namhee Kim, Christian Laing, Shereef Elmetwaly, Segun Jung, Jeremy Curuksu, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

A current challenge in RNA structure prediction is the description of global helical arrangements compatible with a given secondary structure. Here we address this problem by developing a hierarchical graph sampling/data mining approach to reduce conformational space and accelerate global sampling of candidate topologies. Starting from a 2D structure, we construct an initial graph from size measures deduced from solved RNAs and junction topologies predicted by our data-mining algorithm RNAJAG trained on known RNAs. We sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. Graph sampling results for 30 representative RNAs are analyzed and compared with reference graphs from both solved structures and predicted structures by available programs. This comparison indicates promise for our graph-based sampling approach for characterizing global helical arrangements in large RNAs: graph rmsds range from 2.52 to 28.24 Å for RNAs of size 25- 158 nucleotides, and more than half of our graph predictions improve upon other programs. The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design.

Original languageEnglish (US)
Pages (from-to)4079-4084
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume111
Issue number11
DOIs
StatePublished - Mar 18 2014

Keywords

  • Monte Carlo simulated annealing
  • RNA 3D graph
  • RNA 3D prediction

ASJC Scopus subject areas

  • General

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