title: Structure optimization in an off-lattice protein model.
abstract: We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off-lattice models. For two dimensions we found states with lower energy than previously proposed putative ground states for all chain lengths >/=13. This indicates that PERM has the potential to produce native states also for more realistic protein models. For d=3, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.
authors.affiliation: John-von-Neumann Institute for Computing, Forschungszentrum Jülich, D-52425 Jülich, Germany.
authors.forename: Hsiao-Ping
authors.initials: HP
authors.lastname: Hsu
authors.forename: Vishal
authors.initials: V
authors.lastname: Mehra
authors.forename: Peter
authors.initials: P
authors.lastname: Grassberger