Rotamerically Induced Perturbations

RIP: Large Local Perturbations

In these simulations, RIP is applied with a a rotational temperature of 300K to a protein that has been pre-equilibrated to 300K. A rotational temperature of 300K should reproduce the rotational velocities of sidechains at ~ 5000K.

These perturbations can kick out α-helices and loops that are not tightly bound to the body of the protein.

The flexibility of different regions of a structure can be calculated from an analysis of the trajectories generated by applying RIP to all residues in a protein.