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===Model===
Let ''X'' = {''X''<sub>''b''</sub>, ''X''<sub>''s''</sub>} be the random variables representing the entire protein structure. ''X''<sub>''b''</sub> can be represented by a set of 3-d coordinates of the [[Backbone chain|backbone]] atoms, or equivalently, by a sequence of [[bond length]]s and [[dihedral angle]]s. The probability of a particular [[Protein structure|conformation]] ''x'' can then be written as:
:<math>p(X = x|\Theta) = p(X_b = x_b)p(X_s = x_s|X_b,\Theta), \,</math>
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