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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Dynamic soft pocket. #351

Closed primaryodors closed 9 months ago

primaryodors commented 10 months ago

Numerous fixes included with this PR.

primaryodors commented 10 months ago

The dock that prompted the ignore_double_hydrogen_clashes constant:

OR51E2.beta-ionone.active.dock.txt

https://github.com/primaryodors/primarydock/assets/106125032/165ea130-e992-43d5-b9e1-dea065136c2b

primaryodors commented 10 months ago

Tests are passing, although the two test docks intermittently fail. Test predictions are in development to ultimately replace the plain docks.

On the server, the prediction method is using the active state of OR51E2 and calling it "inactive". Consequently, some agonists are giving negative prediction scores. There is also a problem where aliphatic clashes are not being detected when one clashing atom is a hydrogen and the other is a carbon.