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Article ID: 1028 - Last Modified:

What tools can I use for postprocessing of the Glide docking results?

You can use a variety of Schrödinger products to gain more insight into the results of a docking experiment.

  • If you want to calculate a binding affinity, you can use Prime MM-GBSA, which calculates binding affinities with a continuum solvation model.
  • If you want to develop and use a QSAR model from properties of the poses, you can use the Ligand & Structure-Based Descriptors tool to generate properties, from which you can create a model with Strike.
  • If the results of the docking experiment are unsatisfactory, and you suspect that the partial charges used in the docking are not accurate enough, you can use the Quantum Polarized Ligand Docking workflow to improve the charges. Or if you suspect that the receptor isn't flexible enough in the docking experiment, you can try Induced Fit Docking to allow the protein to relax around the ligand, and redock it.

There are also several scripts on the Script Center, in the Docking Post-Processing category, such as the E-Pharmacophores script for creating an energy-optimized structure-based pharmacophore model.

Keywords: Glide, binding, qsar, induced fit

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#131: Is it possible to generate a structure-based pharmacophore model from the receptor binding site?

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