Protein folding: a benchmark combinatorial optimisation problem

The intention of this work is to briefly describe the protein folding as a field of study and to define a model employed in the field to protein tertiary structure prediction called the hydrophobic polar (HP) model. It is proposed that problem instances of this model can be used as both a benchmark and application problem domain for a broad range of combinational optimisation algorithms. This work will provide sufficient information for the protein-folding novice to gain a preliminary understanding of the nature of the problem, so that it could be addressed by a broad range of canonical probabilistic approximation based global search techniques [Introduction].