Structure optimization in an off-lattice protein model

TL;DR

This paper demonstrates the effectiveness of the PERM algorithm in finding low-energy configurations in an off-lattice protein model, surpassing previous results in 2D and providing new states in 3D for future research.

Contribution

It applies the PERM method to off-lattice protein models in 2D and 3D, achieving lower energy states than previously known in 2D and proposing new candidate states in 3D.

Findings

Lower energy states found in 2D for all chain lengths ≥ 13.

PERM shows potential for realistic protein models.

New putative lowest energy states in 3D for future comparison.

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.