Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.

ABSTRACT:

Motivation

RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information.

Results

We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are 'energetically favorable'. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favora

SUBMITTER: Kucharik M 

PROVIDER: S-EPMC4125618 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature