| Title | Non-gradient, Sequential Algorithm for Simulation of Nascent Polypeptide Folding |
| Publication Type | Conference Paper |
| Year of Publication | 2005 |
| Authors | Znamirowski L |
| Editor | Sunderam V.S. |
| Conference Name | Computational Science – ICCS 2005, 5th International Conference, Proceedings, Part I, LNCS 3514 |
| Publisher | Springer-Verlag |
| Conference Location | Berlin Heildelberg |
| Abstract | In the paper, the method for determining of the conformation of nascent protein folding based on two-phase, sequential simulation approach is presented. In both phases the potential energy of molecule under construction is minimized, however in the first phase the minimization is performed for the structure {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 conformation of protein determines initial condition for a future conformation modifications and plays a crucial role in fixing the biological and chemical features of created protein. The simulation of conformation process is illustrated through the numerical example of nascent protein folding for a selected protein. |
