A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC)
Lattice protein models are a major tool for investigating principles of protein folding. For this purpose, one needs an algorithm that is guaranteed to find the minimal energy conformation in some lattice model (at least for some sequences). So far, there are only algorithm that can find optimal conformations in the cubic lattice. In the more interesting case of the face-centered-cubic lattice (FCC), which is more protein-like, there are no results. One of the reasons is that for finding optimal conformations, one usually applies a branch-and-bound technique, and there are no reasonable bounds known for the FCC. We will give such a bound for Dill's HP-model on the FCC, which can be calculated by a dynamic programming approach.
hp-model lattice proteins protein folding branch-and-bound face-centered-cubic-lattice (fcc)