@InProceedings{Bac:Wil:Clo:PSB2000,
  author =	 {Rolf Backofen and Sebastian Will and Peter Clote},
  title =	 {Algorithmic approach to quantifying the hydrophobic
                  force contribution in protein folding},
  booktitle =	 {Proceedings of the Pacific Symposium on Biocomputing (PSB
                  2000)},
  editor =	 {Russ B. Altman and A. Keith Dunker and Lawrence
                  Hunter and Teri E. Klein},
  pages =	 {92--103},
  year =	 2000,
  volume =	 5,
  abstract =	 {Though the electrostatic, ionic, van der Waals,
                  Lennard-Jones, hydrogen bonding, and other forces
                  play an important role in the energy function
                  minimized at a protein's native state, it is widely
                  believed that the {\em hydrophobic force} is the
                  dominant term in protein folding. In this paper, we
                  attempt to quantify the extent to which the
                  hydrophobic force determines the positions of the
                  backbone $\alpha$-carbon atoms in PDB data, by
                  applying Monte-Carlo and genetic algorithms to
                  determine the predicted conformation with minimum
                  energy, where only the hydrophobic force is
                  considered (i.e. Dill's HP-model, and refinements
                  using Woese's polar requirement). This is done by
                  computing the root mean square deviation between the
                  normalized distance matrix $D = (d_{i,j})$
                  ($d_{i,j}$ is normalized Euclidean distance between
                  residues $r_i$ and $r_j$) for PDB data with that
                  obtained from the output of our algorithms. Our
                  program was run on the database of ancient conserved
                  regions drawn from GenBank 101 generously supplied
                  by W. Gilbert's lab, as well as
                  medium-sized proteins (E. Coli RecA, {\tt 2reb},
                  Erythrocruorin, {\tt 1eca}, and Actinidin {\tt
                  2act}). The root mean square deviation (RMSD)
                  between distance matrices derived from the PDB data
                  and from our program output is quite small, and by
                  comparison with RMSD between PDB data and random
                  coils, allows a quantification of the hydrophobic
                  force contribution Keywords: lattice,
                  face-centered-cubic, hydrophobic force, automorphism
                  },
  user =	 {will}
}