The multiple minima problem in protein structure prediction arises from the large number of structural forms corresponding to the energy states of intra-molecule interactions that represent local or global minima that ensure stability. To indicate an appropriate energy minimum and its related spatial structure by simulating the folding process remains a puzzle that has not been solved using existing methods. The proposition presented herein is related to the necessity of treating the folding process as a mechanism based on multi-criteria optimisation that includes both internal force field and external force field optimisation. The protein folding process proved to be dependent on external environmental conditions. This requires treating the protein folding process as multi-criteria optimisation using the technique called the Pareto front. The need of using the multi-criteria optimisation procedure, as well as the propositions to implement this solution to folding process simulation tools are presented in this study.
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