The identification and the elimination of clashes in the structure of an early-stage intermediate in the protein folding process

The model (under consideration) to simulate the protein folding process assumes two steps: early stage (ES) and late stage (LS). The first is assumed to define the preliminary structure, which when applied to an optimization procedure, may produce the proper structure of the protein. However, the ES model produces the structures with clashes. This work demonstrates the possible solution to remove clashes before proceeding to the LS. Additionally, the presented solution describes mathematically the precession phenomenon, which might be useful in other fields of studies aside from protein folding such as medical imaging, quantum physics, and astronomy.