Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials.

@article{Hoppe2006ClassificationAC,
  title={Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials.},
  author={Christian Hoppe and Christoph Steinbeck and Gerd Wohlfahrt},
  journal={Journal of molecular graphics & modelling},
  year={2006},
  volume={24 5},
  pages={
          328-40
        }
}
We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies… CONTINUE READING
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