Using motion planning to study protein folding pathways
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Robot Motion Planning
Proceedings of the sixth annual international conference on Computational biology
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
Tools for simulating and analyzing RNA folding kinetics
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Simulating protein motions with rigidity analysis
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Predicting experimental quantities in protein folding kinetics using stochastic roadmap simulation
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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We propose a novel, motion planning based approach to approximately map the energy landscape of an RNA molecule. Our method is based on the successful probabilistic roadmap motion planners that we have previously successfully applied to protein folding. The key advantage of our method is that it provides a sparse map that captures the main features of the landscape and which can be analyzed to compute folding kinetics. In this paper, we provide evidence that this approach is also well suited to RNA. We compute population kinetics and transition rates on our roadmaps using the master equation for a few moderately sized RNA and show that our results compare favorably with results of other existing methods.