Phys. Rev. E 59, 970–976 (1999)Folding in two-dimensional off-lattice models of proteinsReceived 2 March 1998; revised 2 June 1998; published in the issue dated January 1999 Off-lattice proteinlike models are constructed in two dimensions so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the rank-ordering-based scheme of the assignment of contact energies typically fails in off-lattice models even though it generates high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to the native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties. © 1999 The American Physical Society URL:
http://link.aps.org/doi/10.1103/PhysRevE.59.970
DOI:
10.1103/PhysRevE.59.970
PACS:
87.15.By, 87.10.+e, 71.28.+d, 71.27.+a
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