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A Probabilistic Model of RNA Conformational Space

Figure 2

BARNACLE: a dynamic Bayesian network (DBN) that models the dihedral angles in an RNA fragment.

In the graph, the nodes represent stochastic variables, and the arrows encode their conditional independencies. That is, the graph structure specifies the form of the joint probability distribution of the variables. The shown DBN represents nine consecutive dihedral angles, where the seven central angles originate from a single nucleotide. Each slice (a column of three variables) corresponds to one dihedral angle in an RNA fragment. The variables in each slice are: an angle identifier, D_j, a hidden variable, H_j, and an angular variable, A_j. The angle identifier keeps track of which dihedral angle (from to ) is represented by a slice, while the angular node models the actual dihedral angle value. The hidden nodes induce dependencies between all angles along the sequence (and not just between angles in consecutive slices).

doi: https://doi.org/10.1371/journal.pcbi.1000406.g002