Evaluation of configurational entropy methods from peptide folding-unfolding simulation.

  title={Evaluation of configurational entropy methods from peptide folding-unfolding simulation.},
  author={Da-Wei Li and Mina Khanlarzadeh and Jinbu Wang and Shuanghong Huo and Rafael Br{\"u}schweiler},
  journal={The journal of physical chemistry. B},
  volume={111 49},
A 4-micros molecular dynamics simulation of the second beta-hairpin of the B1 domain of streptococcal protein G is used to characterize the free energy surface and to evaluate different configurational entropy estimators. From the equilibrium folding-unfolding trajectory, 200 000 conformers are clustered according to their root-mean-square deviation (RMSD). The height of the free energy barrier between pairs of clusters is found to be significantly correlated with their pairwise RMSD. Relative… 

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