In the case of a cofactor existing in the ligand binding site, how do I generate a grid to specify the hydrophobic contact with the cofactor but not the amino acid?

You could include the cofactor with the protein when you generate the grid, and use a hydrophobic constraint. The hydrophobic constraint specifies a region of space with a significant hydrophobic environment (from the cofactor and/or protein). It does not set up a specific contact between the ligand and receptor. However, if ligands are expected to make hydrophobic contacts with the cofactor, there might be a nearby hydrobphobic region that would serve for a constraint.

When running the Ligand Docking job, you'll have to specify the ligand feature that can satisfy the constraint. "Hydrophobic" is one of our pre-defined features (it's the default for hydrophobic constraints). You can customize the SMARTS patterns for your specific ligands, if desired.

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