HOPE: A Homotopy Optimization Method for Protein Structure Prediction

Daniel M. Dunlavy, Dianne P. O'leary, Dmitri Klimov, D. Thirumalai
2005 Journal of Computational Biology  
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
more » ... creasing 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.
doi:10.1089/cmb.2005.12.1275 pmid:16379534 fatcat:vh6nqagqcfgb5i3nmca3zun4gm