title: Protein folding: optimized sequences obtained by simulated breeding in a minimalist model.
abstract: For a minimalist model of protein folding, which we introduced recently, we investigate various methods to obtain folding sequences. A detailed study of random sequences shows that, for this model, such sequences usually do not fold to their ground states during simulations. Straight-forward techniques for the construction of folding sequences, based solely on the target structure, fail. We describe in detail an optimization algorithm, based on genetic algorithms, for the "simulated breeding" of folding sequences in this model. We find that, for any target structure studied, there is not only a single folding sequence but a patch of sequences in sequence space that fold to this structure. In addition, we show that, much as in real proteins, nonhomologous sequences may fold to the same target structure.
authors.affiliation: Institut für Theoretische Chemie, Universität Tübingen, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Ebeling
authors.forename: W
authors.initials: W
authors.lastname: Nadler
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins