Predicting folding pathways between RNA conformational structures guided by RNA stacks.

ABSTRACT:

Background

Accurately predicting low energy barrier folding pathways between conformational secondary structures of an RNA molecule can provide valuable information for understanding its catalytic and regulatory functions. Most existing heuristic algorithms guide the construction of folding pathways by free energies of intermediate structures in the next move during the folding. However due to the size and ruggedness of RNA energy landscape, energy-guided search can become trapped in local optima.

Results

In this paper, we propose an algorithm that guides the construction of folding pathways through the formation and destruction of RNA stacks. Guiding the construction of folding pathways by coarse grained movements of RNA stacks can help reduce the search space and make it e

SUBMITTER: Li Y 

PROVIDER: S-EPMC3402921 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature