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Structure optimization in an off-lattice protein model

Hsiao-Ping Hsu·Vishal Mehra·Peter Grassberger
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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 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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Hsiao-Ping Hsu, Vishal Mehra, Peter Grassberger. 2003-10-10. Structure optimization in an off-lattice protein model. https://doi.org/10.1103/physreve.68.037703

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