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Calculating shape complementarity of ligand and protein

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Calculating shape complementarity of ligand and protein

I am trying to calculate the shape complementarity score between a receptor protein and a ligand using Rosetta Scripts. The receptor protein consists of two ions too in the active site next to the ligand. The ligand atoms are written in the .pdb file as HETATM and with CME residue names. The protein and ions are labeled as chain A and the ligand is chain Z. In the Rosetta script, I define the two residue selectors based on the chain names A and Z and calcualted sc between these two chains. When I run the script, I get an error that no surface is defined for chain Z. Chain A residues are read but not Chain Z (ligand). I played around a bit and defined a few residues of the protein as chain Z and the script ran successfully, without reading the ligand atoms. Kindly assist me on what is the right protocol to calculate shape complementarity between a ligand and a protein. Thanks

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Tue, 2023-01-17 11:29

It sounds like your issue is less the shape complementarity and more that you're not properly reading the CME residue. You likely want to create a params file for your ligand. (See the ligand docking documentation for more details.)

The other possible issue is that the code which is doing the shape complementarity calculations is skipping over the ligand residues, possibly because it's unable to figure out what the intended radii are. The ShapeComplementarity filter in RosettaScripts has an (Boolean) use_rosetta_radii option which tells the calculator to use the LJ radii instead of the Lawrence and Coleman specific radii. This may help with getting shape complementarity measures of ligands.

Mon, 2023-02-06 14:42