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WaterDock-2.0

Please Cite the following two papers:

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin

DOI : https://doi.org/10.1371/journal.pone.0172743

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

DOI : http://dx.doi.org/10.1371/journal.pone.0032036

This is a PyMol Plugin for the original WaterDock and the new and improved WaterDock 2.0 specific for holo structures.

INSTALLATION

There are 3 File. init.py, addwater.py and dockcheck.py

Download all three and place in a folder and follow steps below.

  1. Open PyMol

  2. Plugin --> Plugin Manager --> Install New Plugin --> Install From Local File

  3. Choose the init.py file when prompted

  4. DONE!!

Next time PyMol is restarted, Under Plugin, 2 Options will be available

  1. Apo Waterdock -- The originial WaterDock

  2. Holo Waterdock -- The new pipeline specific to holo structures

Python Dependencies

  1. PyMol ofcourse

  2. MDAnalysis -- (version > 0.13)

  3. numpy -- (any version compatible with the MDAnalysis build)

  4. scipy

Things to Note

  1. The script runs AutoDock Vina through system calls of the command 'vina'. The system checks if the command 'vina' is callable and alerts if it is not. Ensure 'vina' in the system refers to AutoDock Vina.

  2. For the Holo-Dock, Please ensure the ligand has Hydrogens added to the structure. And inspect the correct protonation states of relevant atoms.

  3. The output file of both WaterDock options is written as 'predictedwaters.pdb'. If 'predictedwaters.pdb' already exists in the folder, it is renamed to 'predictedwaters1.pdb' and the new file is written as 'predictedwaters.pdb'.

For MacPymol Users

  1. Ensure that you have the correct version of python active

sudo port select --list python

This should return something like:-

Available versions for python: none (active) python26-apple python27 python27-apple

You need to make the python27-apple active:-

sudo port select python python27-apple

You can check it is by doing the list option again, but it should be fine, then fire up MacPymol and do the install and the plugin should work (assuming you have vina in your path as well)..

  1. After Installation, copy the two additional files addwater.py and dockcheck.py into the folder you instructed pymol to install the plugin.