search

primaryodors / primarydock

PrimaryOdors.org molecular docker.
Other
6 stars 4 forks source link

Side chain clashes in docks. #415

Open primaryodors opened 9 months ago

primaryodors commented 9 months ago

Sometimes, the docker produces output in which residue side chains have been flexed into impossible positions clashing with other side chains of the protein.

TODO: Find an example.

primaryodors commented 9 months ago

http://primaryodors.net/viewer.php?view=dock&prot=OR51E2&odor=capric_acid&mode=active

Arg262 is clashing with Val195.

primaryodors commented 9 months ago

This seems to be happening in the FYG-motif active model, not in the dock. It may be wise to add a final step in all the active model predictors to flex any clashing side chains just enough to bring their clash energy below some set threshold.