Dean Williams, L; Ramsay Shaw, B; Gupta Williams, N, "In a Model C G Base Pair, One Amino Group Rotates and the Other Does Not", Journal of the American Chemical Society, 1990, 112(2), 829-833, American Chemical Society (ACS) [Gateway.cgi], [doi] [abs].
In this model every base pair is assumed equally likely to define an insertion site (see below).
We calculated the distance between ensembles after one environmental perturbation (de) simulating a random Gaussian variation (up to 20%) over the value of all the energetic parameters that define the model for base pair interactions (i.e., base pairing and stacking).
Mutational robustness (Rm) accounts for structural changes after single-point mutations in the pre-miRNA sequence, whereas environmental robustness (Re) accounts for structural changes after alterations in the energetic parameters implemented in the thermodynamic model for base pair interactions (Layton and Bundschuh 2005).
More generally, Alkan et al. (2006) studied the joint secondary structure prediction problem under three different models: (i) base pair counting, (ii) stacked pair energy model and (iii) loop energy model.
More generally Alkan et al. [ 1] studied the joint secondary structure prediction problem under three different models: 1) base pair counting, 2) stacked pair energy model, and 3) loop energy model.
We call this model "the variable model": unlike the constant model, the per base pair rate of GC→AT (u) and AT→GC (v) mutations vary depending on time.
Bayesian Interference tree was constructed by the MrBayes software version 3.1.2 (Ronquist and Huelsenbeck 2003), using the doublet model for base pairs and the 4 by 4 model for other sites, with nst = 6 and rates = invgamma.
Therefore, we compute the Borcherdt factors for the GRNN model based the pair of site proxies (left( {f_{0},V_{{{text{S}}30}} } right)), which proves to be fairly efficient.
Of the different types of RNA model, we find that models describing general base pair stability, rather than the precise identity of base pairs, tend to provide a better fit than other RNA models.
