Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
Fig 2
Error in the position as a function of the number of side chain states, resulting from a decomposition of rotamer states into coarse-grained states.
The table summarizes the number of states chosen for each amino acid type. The relative uncertainty is the positional uncertainty for each number of states divided by the accuracy at three states. One, three, or six rotamer states are used, depending on the residue type. For residues without a rotatable χ2, such as valine, only three states are needed. The time to compute the pairwise interactions and solve for the free energy scales roughly as the number of coarse rotamer states squared, so the use of fewer coarse states is preferred. Ile, Leu and Lys are the three residues with rotatable χ2 where only 3 states are assigned.