title: Funnel sculpting for in silico assembly of secondary structure elements of proteins.
abstract: We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of alpha, beta, and alphabeta structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of the foldability of an energy landscape in silico and present an alternative way to view energy landscapes.
authors.affiliation: Department of Structural Biology, Stanford University, Stanford, CA 94305, USA. bfain@stanford.edu
authors.forename: Boris
authors.initials: B
authors.lastname: Fain
authors.forename: Michael
authors.initials: M
authors.lastname: Levitt
mesh_terms: D000465:Algorithms; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins