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Folding in two-dimenensional off-lattice models of proteins

Mai Suan Li·Marek Cieplak
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Abstract

Model off-lattice sequences in two dimensions are constructed 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.

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Mai Suan Li, Marek Cieplak. 1999-08-12. Folding in two-dimenensional off-lattice models of proteins. https://doi.org/10.1103/physreve.59.970

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