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

For many years, scientists have been trying to unravel the protein folding process. This paper presents a proposition of an improvement to one of models trying to describe it, the elliptical model, developed by the Department of Bioinformatics and Telemedicine UJ-CM [22]. The model assumes a division of a protein folding process into two stages: the Early-Stage (ES) and the Late-Stage (LS). After the first stage, the second one sometimes occurs unable to perform, because of accidentally created clashes between atoms. This work demonstrates several possible solutions to remove clashes before proceeding to the LS. Additionally, one of presented solutions describes mathematically the precession phenomenon, what might be useful in other than protein folding field of studies such as medical imaging, quantum physics or astronomy.