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

@article{Herges2005InSF,
  title={In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.},
  author={Thomas Herges and Wolfgang Wenzel},
  journal={Physical review letters},
  year={2005},
  volume={94 1},
  pages={
          018101
        }
}
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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