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Bioinformatics Advance Access published online on June 25, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn328
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

iFoldRNA: Three-dimensional RNA Structure Prediction and Folding

Shantanu Sharma 1, Feng Ding 1 and Nikolay V. Dokholyan 1,*

1Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA

*To whom correspondence should be addressed. Prof. Nikolay V. Dokholyan, E-mail: dokh{at}med.unc.edu


  Abstract

Summary: Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input RNA sequences. Starting from simplified linear-chain conformations, RNA molecules (<50 nucleotides) fold to native-like structures within half an hour of simulation, facilitating rapid RNA structure prediction. All-atom reconstruction of energetically stable conformations generates iFoldRNA predicted RNA structures. The predicted RNA structures are within 2-5 Angstrom root mean square deviations from corresponding experimentally derived structures. RNA folding parameters including specific heat, contact maps, simulation trajectories, gyration radii, root mean square deviations from native state, fraction of native-like contacts are accessible from iFoldRNA. We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses.

Availability: http://iFoldRNA.dokhlab.org.

Contact: dokh{at}med.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online

Associate Editor: Prof. Ivo Hofacker

Received on April 11, 2008; revised on June 13, 2008; accepted on June 22, 2008

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