Applications To Protein Structure Prediction
Dead-end elimination has been used effectively to predict the structure of side chains on a given protein backbone structure by minimizing an energy function . The dihedral angle search space of the side chains is restricted to a discrete set of rotamers for each amino acid position in the protein (which is, obviously, of fixed length). The original DEE description included criteria for the elimination of single rotamers and of rotamer pairs, although this can be expanded.
In the following discussion, let be the length of the protein and let represent the rotamer of the side chain. Since atoms in proteins are assumed to interact only by two-body potentials, the energy may be written
Where represents the "self-energy" of a particular rotamer, and represents the "pair energy" of the rotamers .
Also note that (that is, the pair energy between a rotamer and itself) is taken to be zero, and thus does not affect the summations. This notation simplifies the description of the pairs criterion below.
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