Identifying the protein folding nucleus using molecular dynamics
  Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their appearance determines folding cooperativity and drives the model protein into its folded conformation. 
Nikolay V. Dokholyan (1), Sergey V. Buldyrev (1), H. Eugene Stanley   (1) and Eugene I. Shakhnovich(2) ((1) Center for Polym...