HOPE: A Homotopy Optimization Method for Protein Structure Prediction

TitleHOPE: A Homotopy Optimization Method for Protein Structure Prediction
Publication TypeJournal Articles
Year of Publication2005
AuthorsDunlavy DM, O'Leary DP, Klimov D, Thirumalai D
JournalJournal of Computational Biology
Pagination1275 - 1288
Date Published2005/12//
ISBN Number1066-5277, 1557-8666

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.