CyloFold: secondary structure prediction including pseudoknots.

ABSTRACT:

Unlabelled

Computational RNA secondary structure prediction approaches differ by the way RNA pseudoknot interactions are handled. For reasons of computational efficiency, most approaches only allow a limited class of pseudoknot interactions or are not considering them at all. Here we present a computational method for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity. The approach is based on simulating a folding process in a coarse-grained manner by choosing helices based on established energy rules. The steric feasibility of the chosen set of helices is checked during the folding process using a highly coarse-grained 3D model of the RNA structures. Using two data sets of 26 and 241 RNA sequences we find that this approach is competitive c

SUBMITTER: Bindewald E 

PROVIDER: S-EPMC2896150 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature