Efficient computation of RNA folding dynamics
- 15 April 2004
- journal article
- Published by IOP Publishing in Journal of Physics A: General Physics
- Vol. 37 (17) , 4731-4741
- https://doi.org/10.1088/0305-4470/37/17/005
Abstract
Barrier trees consisting of local minima and their connecting saddle points imply a natural coarse-graining for the description of the energy landscape of RNA secondary structures. Here we show that, based on this approach, it is possible to predict the folding behaviour of RNA molecules by numerical integration. Comparison with stochastic folding simulations shows reasonable agreement of the resulting folding dynamics and a drastic increase in computational efficiency that makes it possible to investigate the folding dynamics of RNA of at least tRNA size. Our approach is readily applicable to bistable RNA molecules and promises to facilitate studies on the dynamic behaviour of RNA switches.Keywords
This publication has 45 references indexed in Scilit:
- All-Atom Structure Prediction and Folding Simulations of a Stable ProteinJournal of the American Chemical Society, 2002
- Engineered allosteric ribozymes as biosensor componentsCurrent Opinion in Biotechnology, 2002
- Barrier Trees of Degenerate LandscapesZeitschrift für Physikalische Chemie, 2002
- EARLY EVENTS IN RNA FOLDINGAnnual Review of Physical Chemistry, 2001
- RNA folding at elementary step resolutionRNA, 2000
- HIERARCHY AND DYNAMICS OF RNA FOLDINGAnnual Review of Biophysics, 1997
- Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformationThe EMBO Journal, 1997
- The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kineticsThe Journal of Chemical Physics, 1997
- Event-Based Relaxation of Continuous Disordered SystemsPhysical Review Letters, 1996
- The Energy Landscapes and Motions of ProteinsScience, 1991