iFoldRNA: three-dimensional RNA structure prediction and folding
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iFoldRNA: three-dimensional RNA structure prediction and folding
iFoldRNA: three-dimensional RNA structure prediction and folding Shantanu Sharma, Feng Ding and Nikolay V. Dokholyan∗ Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Received on April 11, 2008; revised on June 13, 2008; accepted on June 22, 2008 Advance Access publication June 25, 2008 Associate Editor: Ivo Hofacker
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 linearchain conformations, RNA molecules (50 nt (e.g. ribosomal RNA, NDB: 2il9, 142 nt) require significantly longer time scales to sample the exponentially increasing conformational space. This limits the accuracy of the iFoldRNA structure prediction to intermediatelength RNA molecules (
