@InProceedings{Mann:Backofen:Will:_equivalence_classes:WCB09,
  author =       {Martin Mann and Rolf Backofen and Sebastian Will},
  title =        {Equivalence Classes of Optimal Structures in
                  {HP}~Protein Models Including Side Chains}, 
  booktitle =	 {Proceedings of the Fifth Workshop on Constraint 
                  Based Methods for Bioinformatics (WCB09)},
  year =	 2009,
  arxiv =    	 {0910.3848},
  user =	 {will},
  abstract =	 {Lattice protein models, as the Hydrophobic-Polar
                  (HP) model, are a common abstraction to enable
                  exhaustive studies on structure, function, or
                  evolution of proteins. A main issue is the high
                  number of optimal structures, resulting from the
                  hydrophobicity-based energy function applied. We
                  introduce an equivalence relation on protein
                  structures that correlates to the energy
                  function. We discuss the efficient enumeration of
                  optimal representatives of the corresponding
                  equivalence classes and the application of the
                  results.}
}