Optimally compact finite sphere packings - Hydrophobic cores in the FCC

Abstract

Lattice protein models are used for hierarchical approaches to protein structure prediction, as well as for investigating principles of protein folding. The problem is that there is so far no known lattice that can model real protein conformations with good quality, and for which there is an eficient method to prove whether a conformation found by some heuristic algorithm is optimal. We present such a method for the FCC-HP-Model [3]. For the FCC-HP-Model, we need to find conformations with a maximally compact hydrophobic core. Our method allows us to enumerate maximally compact hydrophobic cores for suficiently great number of hydrophobic amino-acids. We have used our method to prove the optimality of heuristically predicted structures for HP-sequences in the FCC-HP-model.