In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field - PubMed

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field

T Herges et al. Phys Rev Lett. 2005.

Abstract

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

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