This work studies the build-up method for the global minimization problem for molecular conformation, especially protein folding. The problem is hard to solve for large molecules using general minimization approaches because of the enormous amount of required computation. A prototype algorithm is designed using the anisotropic effective energy simulated annealing method at each build-up stage.
Optimization problems take different forms arising from the motivating applications.
A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing. Technical Report CTC93TR130, ACRI, Cornell University, 1993. Doc 1014 Optimization by Simulated Annealing - Kirkpatrick, Gellat et al. Doc 5 Journal of Physical Chemistry - the, Method et al. Doc 2 Journal of Chemical Physics - State, fast et al.