Protein Folding in the 2D HP Model

We study folding algorithms in the two-dimensional Hydrophobic- Hydrophilic model (2D HP model) for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show that two of the generalizations do not improve the worst case approximation ratio. The third generalization seems to be better, and the analysis of its approximation ratio leads to an interesting combinatorial problem.

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