Using motion planning to study RNA folding kinetics Conference Paper uri icon

abstract

  • 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.

name of conference

  • Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04

published proceedings

  • Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04

author list (cited authors)

  • Tang, X., Kirkpatrick, B., Thomas, S., Song, G., & Amato, N. M.

citation count

  • 35

complete list of authors

  • Tang, Xinyu||Kirkpatrick, Bonnie||Thomas, Shawna||Song, Guang||Amato, Nancy M

publication date

  • January 2004