A Novel Algorithm to Predict Bridging Water Locations During Computational Ligand Docking

Last updated: 5/7/2019

---

XMLs

• timing_low_res_pw.xml

  XML script used to generate low-resolution trials and the PlaceWaters trials. If you only want to generate the low-resolution trials without PlaceWaters mover, remove the
  "<Add mover_name="pack_rotamers_mover"/>" and "<Add mover_name="place_waters"/>" lines. This XML also contains the timing metrics used to collect information on the duration of each mover, which can be removed.

• timing_high_res.xml

  XML script for the high-resolution and final minimization steps, intended to go after the PlaceWaters mover. Requires that the ligand is on chain "X" and the waters are on chain "W".

Python scripts

• rank_native_waters.py

  Used to determine which waters in the PDB were "bridging waters", defined as being within 3 of both the ligand and protein. Produces a "pruned" pdb file with only the bridging waters.

• tune_params.py

  Script used to train the parameters on the training set. Contains the loss function as well as the range of each variable tested.

• random_waters.py

  Used in place of the PlaceWaters in the random water placement trials. Randomly places between 1 and 5 waters around the ligand.

• fix_chains.py

  Moves waters to chain "W" and updates the atom numbers and residue numbers accordingly. Also removes unnecessary "TERM" lines.