Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.

@article{Wang1999RankingLB,
  title={Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study.},
  author={Jennifer Y. Wang and Richard W. Dixon and Peter A. Kollman},
  journal={Proteins},
  year={1999},
  volume={34 1},
  pages={
          69-81
        }
}
The binding of 14 biotin analogues to avidin is examined to evaluate the viability of calculating binding free energy based on molecular dynamics (MD) trajectories. Two approaches were investigated in this work. The first one uses the linear interaction energy approximation, while the other approach utilizes the interaction free energy. The results obtained from these two methods were found to correlate well with the experimental binding free energy data for 10 out of 14 ligands. For the other… CONTINUE READING

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