Introduction

This tutorial shows how to detect water molecules that might form hydrogen bonds with protein structures (called water bridges). The prediction method introduced here helps evaluate the significance of water molecules on the stability and dynamics of protein structure.

Required Programs

The latest version of ProDy is required.

Recommended Programs

Besides ProDy, the Matplotlib library and VMD program are required for some steps in the tutorial. IPython is highly recommended for interactive usage.

Moreover, in the case of the lack of hydrogen atoms in protein structures, additional packages such as Openbabel or PDBfixer are required to predict hydrogen bonds.

They can be installed using a conda or pip.

Getting Started

To follow this tutorial, you will need the following files:

1.5M Feb 29  2024 5kqm_all_sci.pdb
446K Feb 29  2024 addH_5kqm.pdb
2.9M Aug  5 10:24 case_study1.pdb
1.5M Aug  5 10:24 case_study4a.pdb
1.5M Aug  5 10:24 case_study4b.pdb
3.8M Feb 29  2024 NAMD_D2_sample.dcd
 78M Feb 29  2024 pebp1_50frames.pdb

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy and Matplotlib packages.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: import matplotlib

We have included these imports in every part of the tutorial so that the code copied from the online pages is complete. You do not need to repeat imports in the same Python session.

How to Cite

If you benefited from WatFinder Calculations in your research, please cite the following paper:

[JK24]

Krieger JM, Doljanin F, Bogetti AT, Zhang F, Manivarma T, Bahar I, Mikulska-Ruminska K. WatFinder: A ProDy tool for protein-water interactions. Bioinformatics 2024 btae516.