title: HOPE: a homotopy optimization method for protein structure prediction.
abstract: We use a homotopy optimization method, HOPE, to minimize the potential energy associated with a protein model. The method uses the minimum energy conformation of one protein as a template to predict the lowest energy structure of a query sequence. This objective is achieved by following a path of conformations determined by a homotopy between the potential energy functions for the two proteins. Ensembles of solutions are produced by perturbing conformations along the path, increasing the likelihood of predicting correct structures. Successful results are presented for pairs of homologous proteins, where HOPE is compared to a variant of Newton's method and to simulated annealing.
authors.affiliation: Applied Mathematics and Scientific Computation Program, University of Maryland, College Park, 20742, USA. ddunlavy@cs.umd.edu
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Dunlavy
authors.forename: Dianne P
authors.initials: DP
authors.lastname: O'Leary
authors.forename: Dmitri
authors.initials: D
authors.lastname: Klimov
authors.forename: D
authors.initials: D
authors.lastname: Thirumalai
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D030562:Databases, Protein; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins