Folding of a 16-residue helical peptide using molecular dynamics simulation with Tsallis effective potential

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Abstract
We have demonstrated that a molecular dynamics simulation method in conjunction with a Tsallis effective potential enables a 16-residue model peptide to fold into a complete α-helix in a reasonably short time. The current study also indicates that one can practically observe reversible foldings of the peptide with the method, mainly due to its superior capability of overcoming potential energy barriers. Therefore it is anticipated that the new method may provide a quite efficient conformational searching tool for systems with many degrees of freedom such as proteins and DNAs.