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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Adjust best binding algorithm to preferentially pair ligand aldehydes with basic side chains. #258

Open primaryodors opened 1 year ago

primaryodors commented 1 year ago 
          The best-binding is failing for aldehydes. It should favor pairing them with basic side chains, but it is pairing them to acids instead.

Originally posted by @ssepeq in https://github.com/primaryodors/primarydock/issues/254#issuecomment-1565826290

One example to test with may be Lys80 of OR1G1 with an octanal or decanal ligand. Another may be the His residues in the binding pocket of OR1A1 and any of that receptor's aldehyde agonist ligands.

primaryodors commented 1 year ago

262

electronicsbyjulie commented 1 year ago

This might not be working.

Also, the same behavior should be applied to tumble spheres.