@InProceedings{Will:PSB2002,
  author =	 {Sebastian Will},
  title =	 {Constraint-based Hydrophobic Core Construction for
                  Protein Structure Prediction in the
                  Face-Centered-Cubic Lattice},
  booktitle =	 {Proceedings of the Pacific Symposium on Biocomputing
                  2002 (PSB 2002)},
  editor =	 {Russ B. Altman and A. Keith Dunker and Lawrence
                  Hunter and Teri E. Klein},
  publisher =	 {World Scientific Publishing Co. Pte. Ltd.},
  address =	 {Singapore},
  year =	 2002,
  pages =	 {661--672},
  pmid =	 {11928518},
  abstract =	 {We present an algorithm for exact protein structure
                  prediction in the FCC-HP-model. This model is a
                  lattice protein model on the face-centered-cubic
                  lattice that models the main force of protein
                  folding, namely the hydrophobic force. The structure
                  prediction for this model can be based on the
                  construction of hydrophobic cores. The main focus of
                  the paper is on an algorithm for constructing
                  maximally and submaximally compact hydrophobic cores
                  of a given size. This algorithm treats core
                  construction as a constraint satisfaction problem
                  (CSP), and the paper describes its constraint
                  model. The algorithm employs symmetry excluding
                  constraint-based search [Backofen, Will: CP99] and
                  relies heavily on good upper bounds on the number of
                  contacts. Here, we use and strengthen upper bounds
                  presented earlier. [Backofen, Will: CPM2001] The
                  resulting structure prediction algorithm (including
                  previous work [Backofen, Will: CPM2001, Backofen,
                  Will: CP2001]) handles sequences of sizes in the
                  range of real proteins fast, i.e. we predict a first
                  structure often within a few minutes. The algorithm
                  is the first exact one for the FCC, besides full
                  enumeration which is impracticable for chain lengths
                  greater than about 15. We tested the algorithm
                  succesfully up to sequence length of 160, which is
                  far beyond the capabilities even of previous
                  heuristic approaches.},
  user =	 {will}
}