title: Predicting helical coaxial stacking in RNA multibranch loops.
abstract: The hypothesis that RNA coaxial stacking can be predicted by free energy minimization using nearest-neighbor parameters is tested. The results show 58.2% positive predictive value (PPV) and 65.7% sensitivity for accuracy of the lowest free energy configuration compared with crystal structures. The probability of each stacking configuration can be predicted using a partition function calculation. Based on the dependence of accuracy on the calculated probability of the stacks, a probability threshold of 0.7 was chosen for predicting coaxial stacks. When scoring these likely stacks, the PPV was 66.7% at a sensitivity of 51.9%. It is observed that the coaxial stacks of helices that are not separated by unpaired nucleotides can be predicted with a significantly higher accuracy (74.0% PPV, 66.1% sensitivity) than the coaxial stacks mediated by noncanonical base pairs (55.9% PPV, 36.5% sensitivity). It is also shown that the prediction accuracy does not show any obvious trend with multibranch loop complexity as measured by three different parameters.
authors.affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
authors.forename: Rahul
authors.initials: R
authors.lastname: Tyagi
authors.forename: David H
authors.initials: DH
authors.lastname: Mathews
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012335:RNA, Ribosomal; D012313:RNA