Structure optimization in an off-lattice protein model

Details Structure optimization in an off-lattice protein model Structure optimization in an off-lattice protein model

2003-02-26

arxiv.org/abs/cond-mat/0302545v2

Phys. Rev. E 68, 037703 (2003)

Physics

Condensed Matter

Statistical Mechanics

4 pages, 2 figures

Scientific paper

10.1103/PhysRevE.68.037703

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 2 dimensions we found states with lower energy than previously proposed putative ground states, for all chain lengths $\ge 13$. 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.

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