@Article{Bac:Wil:Bor:BioInfo99,
  author =       "Rolf Backofen and Sebastian Will and Erich Bornberg-Bauer",
  title =        "Application of Constraint Programming Techniques for
                  Structure Prediction of Lattice Proteins with Extended
                  Alphabets",
  journal =      "Bioinformatics",
  year =         1999,
  volume =       15,
  number =       3,
  pages   =      "234-242",
  abstract = {Predicting the ground state of biopolymers is a
  notoriously hard problem in biocomputing.  Model systems, such as
  lattice proteins are simple tools and valuable to test and improve
  new methods.  Best known are HP-type models with sequences composed
  from a binary (hydrophobic and polar) alphabet.  Major drawback is
  the degeneracy, i.e. the number of different ground state
  conformations.  
  
  Here we show how recently developed constraint
  programming techniques can be used to solve the structure prediction
  problem efficiently for a higher order alphabet.  To our knowledge
  it is the first report of an exact and computationally feasible
  solution to model proteins of length up to 36 and without resorting
  to maximally compact states.  We further show that degeneracy is
  reduced by more than one order of magnitude and that ground state
  conformations are not necessarily compact.  Therefore, more
  realistic protein simulations become feasible with our model.},
  user =	 {will}
}