Folding in two-dimensional off-lattice models of proteins

Off-lattice proteinlike models are constructed in two dimensions so that th eir native states are close to an on-lattice target. The Hamiltonian involv es the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carl o processes. The sequences are characterized thermodynamically and kinetica lly. It is shown that the rank-ordering-based scheme of the assignment of c ontact energies typically fails in off-lattice models even though it genera tes high stability of on-lattice sequences. Similar to the on-lattice case, Go-like modeling, in which the interaction potentials are restricted to th e native contacts in a target shape, gives rise to good folding properties. Involving other contacts deteriorates these properties. [S1063-651X(99)053 01-5].