Empirical potentials and functions for protein folding and binding.

@article{Vajda1997EmpiricalPA,
  title={Empirical potentials and functions for protein folding and binding.},
  author={S. Vajda and M. Sippl and J. Novotn{\'y}},
  journal={Current opinion in structural biology},
  year={1997},
  volume={7 2},
  pages={
          222-8
        }
}
  • S. Vajda, M. Sippl, J. Novotný
  • Published 1997
  • Chemistry, Medicine
  • Current opinion in structural biology
  • Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations to the latter. The potentials that have been used in the free-energy ranking of protein-ligand… CONTINUE READING
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    References

    SHOWING 1-10 OF 83 REFERENCES
    Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
    • 68
    Prediction of protein complexes using empirical free energy functions
    • 86
    • PDF
    A continuum model for protein-protein interactions: application to the docking problem.
    • 159
    Principles of protein folding — A perspective from simple exact models
    • 1,304
    • PDF
    Statistical potentials extracted from protein structures: how accurate are they?
    • 397
    • PDF
    Structure-derived potentials and protein simulations.
    • 262
    • PDF