Network Properties of the Ensemble of RNA Structures.
We describe the first dynamic programming algorithm that computes the expected degree for the network, or graph G = (V, E) of all secondary structures of a given RNA sequence a = a1, …, an. Here, the nodes V correspond to all secondary structures of a, while an edge exists between nodes s, t if the secondary structure t can be obtained from s by adding, removing or shifting a base pair. Since secondary structure kinetics programs implement the Gillespie algorithm, which simulates a random walk on the network of secondary structures, the expected network degree may provide a better understanding of kinetics of RNA folding when allowing defect diffusion, helix zippering, and related conformation transformations. We determine the correlation between expected network degree, contact order, conformational entropy, and expected number of native contacts for a benchmarking dataset of RNAs. Source code is available at http://bioinformatics.bc.edu/clotelab/RNAexpNumNbors.
Department of Biology, Boston College, Chestnut Hill, MA 02467 United States of America.
Peter
P
Clote
Department of Biology, Boston College, Chestnut Hill, MA 02467 United States of America.
Amir
A
Bayegan
D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding
D012313:RNA