search

primaryodors / primarydock

PrimaryOdors.org molecular docker.
Other
6 stars 3 forks source link

Histidine protonation for OR51E2 #388

Closed primaryodors closed 7 months ago

primaryodors commented 8 months ago

Allows acid ligands to protonate histidine side chains for example in OR51E2 where His180 would most likely be protonated according to the cryo-EM model.

primaryodors commented 8 months ago

All tests passing. Waiting for a new set of results from the cron.

primaryodors commented 8 months ago

Ligand placement looks good w.r.t. His180 and Arg262. However, the histidine is not protonated despite being within range for a hydrogen bond on the Nδ tautomer.

OR51E2.propionic_acid.active.dock.txt

Predictions on OR51E2 are of moderate accuracy. Predictions on OR51E1 are poor.

Scoring function of primarydock app varies from output of score_pdb utility. The docker app is not recognizing the full strength of the ligand's ionic bond to Arg262.

primaryodors commented 7 months ago

All unit tests successful.