WaterDock2.0

This is an updated to Python3 version of WaterDock2.0 https://github.com/bigginlab/WaterDock-2.0

Original Python2 version of WaterDock2.0 written by Akshay Sridhar (https://doi.org/10.1371/journal.pone.0172743) based on the original WaterDock method developed by Greg Ross (https://doi.org/10.1371/journal.pone.0032036) Comments and queuries should be address to philip.biggin@bioch.ox.ac.uk

This is a Command line interface of WaterDock2.0 for python

python waterdock2.py proteinfile.pdbqt ligandfile.pdb

This will output a single file called "predictedwaters.pdb", which contains the predictions of the oxygen positions.

Example input files are included as example-protein.pdbqt and example-ligand.pdb

-- MDAnalysis (version >= 0.13)

-- numpy (any version compatible with your MDAnalysis build)

-- scipy (version does not matter)

-- vina (note on Mac Catalina, you may have to obtain the 64bit version directly from http://vina.scripps.edu/download.html)

Protein File -- pdbqt - the Autodock format of a PDB with charge (Q) and atom type (T)

Ligand File -- pdb/mol2 sybyl mol2 format

Note that both the ligand and the protein file should have the correction protonation state.

To generate the receptor pdbqt file, we recommend AutoDockTools (ADT - get MGLTools from http://mgltools.scripps.edu/downloads), but if you are on a Mac with Catalina there is currently no 64-bit version. In that case you might be avle to use the AFR package (see here https://ccsb.scripps.edu/adfr/how-to-create-a-pdbqt-for-my-receptor/)

An example protein (example-protein.pdbqt) and an example ligand are provide (example-ligand.pdb)

python waterdock2.py example-protein.pdbqt example-ligand.pdb

will generate predictedwaters.pdb which should contain 3 predicted water molecule locations.

You can check the result of the prediction in pymol or compare it directly to the file "expected-predictedwaters.pdb"