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Article ID: 1458 - Last Modified: August 16, 2011

What can I do to get better docking results from a homology model?

Here are a few things you can try to get better results docking against your homology model:

  • Consider refining loops that are in the vicinity of the active site, especially if they did not have high sequence identity. (If the loops were built from a region with high sequence identity, this may be less important.) You can use the Prime Refinement panel. For loop pairs that are in physical contact with one another, you can perform a cooperative loop sampling.
  • Use Induced Fit Docking (IFD) to refine the active site. IFD performs flexible-ligand/flexible-receptor docking. Side chains are rearranged, and the backbone will relax upon minimization. However, loops are not conformationally sampled. You may wish to omit conformational sampling of side chains in regions that have low B-factors in the template structure and also come from a region with high sequence identity. If you have multiple classes of known active ligands, consider running IFD on multiple compounds.
  • When setting up Glide grids, apply hydroxyl sampling to active site OH groups by selecting "Allow rotation of receptor hydroxyl groups" in the Rotatable Groups tab.
  • Using the Virtual Screening Workflow, run ensemble docking against multiple receptor structures created by IFD. Note that different active site conformations may retrieve different classes of active ligands.

Keywords: Prime, Glide, IFD, VSW

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