Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

@article{Liang2011ProteinSC,
  title={Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions},
  author={Shide Liang and Yaoqi Zhou and Nick V. Grishin and Daron M. Standley},
  journal={Journal of computational chemistry},
  year={2011},
  volume={32 8},
  pages={1680-6}
}
We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance-dependent energy functions (OSCAR-d) and side-chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conformations from non-native conformations, using a training set of 12,000 side chains for each residue… CONTINUE READING