title: Structure-based design of model proteins.
abstract: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model.
authors.affiliation: Department of Physics and Center for Materials Physics, Pennsylvania State University, University Park, USA.
authors.forename: J R
authors.initials: JR
authors.lastname: Banavar
authors.forename: M
authors.initials: M
authors.lastname: Cieplak
authors.forename: A
authors.initials: A
authors.lastname: Maritan
authors.forename: G
authors.initials: G
authors.lastname: Nadig
authors.forename: F
authors.initials: F
authors.lastname: Seno
authors.forename: S
authors.initials: S
authors.lastname: Vishveshwara
mesh_terms: D000595:Amino Acid Sequence; D008958:Models, Molecular; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins