Abstract
In this paper, we find ‘good’ amino acid sequences that fold to a desired “target” structure as a ground state conformation of lowest accessible free energy using the modified bond-fluctuation lattice model. In our protein lattice model, bond lengths are set to vary between one and √2 in three dimensions. Our results agree well with the native state energies EN. Comparisons with the “putative native state” (PNS) energy EPNS and the “hydrophobic zippers” (HZ) energy EHZ are made. For every sequence, the global energy minimum is found to have multiple degeneracy of conformations, which is the same result as for the constraint-based hydrophobic core construction (CHCC) method. The interior conformations of the ground states are also discussed.
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