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docking-org / pydock3

Python package wrapping the DOCK Fortran program and providing several tools built on top of it.
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Add tarting optimization to DockOpt #15

Open ianscottknight opened 2 years ago

ianscottknight commented 2 years ago

It seems that the practice of "tarting" can be a very effective way of improving the quality of docking configurations as evaluated by retrospective docking. Incorporating tarting as a new set of parameters may prove especially helpful in enabling DockOpt to find good docking configurations.

ianscottknight commented 2 years ago

https://wiki.docking.org/index.php/DOCK_3.7_tart

According to this, the process of tarting is:

  1. Rename 3-letter residue code of target residue in rec.crg.pdb to be different from all canonical residue codes (e.g. MET --> MEU)
  2. Add said residue code to prot.table.ambcrg.ambH with modified charge distribution across residue atoms
  3. Replace representation of original residue in amb.crg.oxt with new one
ianscottknight commented 2 years ago

~Note that this issue depends on #5 being completed first.~ #5 complete.

ianscottknight commented 1 year ago

@gregorpatof (Olivier Mailhot) has made strides in automating tarting optimization. Assigning him to this issue for collaboration.