An example of the shortened sidechains of LYS and ARG. Only the first four heavy atoms of the sidechain (drawn in heavy lines) are considered in the energy expression.
An outline of the six step sidechain addition method appears on the following slides. The method uses 215 sidechain rotamers. A rotamer is a fixed sidechain position determined by the first two torsions along the side chain. A long sidechain may have as many as 16 rotamers in our database while alanine and glycine have none.
While other rotamer methods rely on a large rotamer library (at least 500 or more) and a simple hard-sphere model of atomic forces, our method utilizes a more complex Morse function that allows a “softer” nonbond interaction between atoms nearby in space. This helps to prevent dismissing candidate near native rotamers that would otherwise be ignored due to a single bad interaction that could be resolved with a slight minimization.
A second approximation of our method is to only include the first two sidechain torsion angles within our database (see figure below). This results in an energy function that only examines the first four heavy atoms of the sidechain for LYS and ARG. Since these two sidechains are long and have many more degrees of freedom to relax within the protein, “snipping” off the ends helps to avoid bad contacts during the selection phase that can easily be remedied with a small amount of minimization.