MOPED: Method for optimizing physical energy parameters using decoys

Chaok Seok, J. B. Rosen, John D. Chodera, and Ken A. Dill. 
J. Comput. Chem., 24(1):89-97 (2003) [DOI] [PDF]

We show how the long-time dynamics of biomolecular systems can be recapitulated from statistics collected from short molecular simulations sampling transitions between kinetically metastable states.