title: A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles.
abstract: We discuss a computational approach for reconstructing the native structures of proteins from the knowledge of a structural profile - the first eigenvector of the contact map of the native structure itself. The procedure consists in carrying out Monte Carlo simulations of a tube model of the protein structure with an energy bias towards the target structural profile. We present the reconstruction of two small proteins and address problems arising in the reconstruction of larger proteins. Our results indicate that an accurate physico-chemical energy function should be used in conjunction with the structural profile bias in order to achieve accurate reconstructions.
authors.affiliation: Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Wolff
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
authors.forename: Markus
authors.initials: M
authors.lastname: Porto
mesh_terms: D008958:Models, Molecular; D009010:Monte Carlo Method; D017434:Protein Structure, Tertiary / Q000502:physiology; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013816:Thermodynamics
chemical_list: D011506:Proteins