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In the paper, the method for determining of the conformation of nas cent protein folding based on two-phase, sequential simulation approach is pre sented. In both phases the po tential energy of molecule under construction is mini mized, however in the first phase the minimization is performed for the struc ture {new amino acid}/{existing amino acid chain} and in the second phase, the {new existing amino acid chain} conformation is “tuned” to reach the minimal potential energy of growing chain. The formed, nascent con for ma tion of protein deter mines initial condition for a future conformation mo di fi ca tions and plays a crucial role in fixing the biologi cal and chemical featu res of created protein. The si mu lation of conformation process is illustrated through the numerical example of nascent protein folding for a selected protein.

Non-gradient, Sequential Algorithm for Simulation of Nascent Polypeptide Folding