Coarse-grained prediction of RNA loop structures.

ABSTRACT: One of the key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the sequence. RNA loop free energies are dependent on the loop sequence content. However, most current models account only for the loop length-dependence. The previously developed "Vfold" model (a coarse-grained RNA folding model) provides an effective method to generate the complete ensemble of coarse-grained RNA loop and junction conformations. However, due to the lack of sequence-dependent scoring parameters, the method is unable to identify the native and near-native structures from the sequence. In this study, using a previously developed iterative method for extracting the knowledge-based potential parameters from the known structures, we derive a set of dinucleotide-based stat

SUBMITTER: Liu L 

PROVIDER: S-EPMC3493578 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature