Design of protein-ligand binding based on the molecular-mechanics energy model.

@article{Boas2008DesignOP,
  title={Design of protein-ligand binding based on the molecular-mechanics energy model.},
  author={F. Edward Boas and Pehr A B Harbury},
  journal={Journal of molecular biology},
  year={2008},
  volume={380 2},
  pages={415-24}
}
While the molecular-mechanics field has standardized on a few potential energy functions, computational protein design efforts are based on potentials that are unique to individual laboratories. Here we show that a standard molecular-mechanics potential energy function without any modifications can be used to engineer protein-ligand binding. A molecular-mechanics potential is used to reconstruct the coordinates of various binding sites with an average root-mean-square error of 0.61 A and to… CONTINUE READING