Solving the HP model with Nested Monte Carlo Search
This is an incremental contribution to protein folding simulation methods for computational biology researchers.
The authors developed a new Monte Carlo Search algorithm for finding the ground state energy of proteins in the HP-model, but it does not outperform existing state-of-the-art methods like PERM, REMC, or WLRE.
In this paper we present a new Monte Carlo Search (MCS) algorithm for finding the ground state energy of proteins in the HP-model. We also compare it briefly to other MCS algorithms not usually used on the HP-model and provide an overview of the algorithms used on HP-model. The algorithm presented in this paper does not beat state of the art algorithms, see PERM (Hsu and Grassberger 2011), REMC (Thachuk, Shmygelska, and Hoos 2007) or WLRE (Wüst and Landau 2012) for better results. Hsu, H.-P.; and Grassberger, P. 2011. A review of Monte Carlo simulations of polymers with PERM. Journal of Statistical Physics, 144 (3): 597 to 637. Thachuk, C.; Shmygelska, A.; and Hoos, H. H. 2007. A replica exchange Monte Carlo algorithm for protein folding in the HP model. BMC Bioinformatics, 8(1): 342. Wüst, T.; and Landau, D. P. 2012. Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins. The Journal of Chemical Physics, 137(6): 064903.