The Free Energy Landscape of Small Molecule Unbinding

  title={The Free Energy Landscape of Small Molecule Unbinding},
  author={Danzhi Huang and Amedeo Caflisch},
  booktitle={PLoS Computational Biology},
The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a… CONTINUE READING
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