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.

Getting Started

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

1.5M Feb 29 20:20 5kqm_all_sci.pdb
446K Feb 29 20:20 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 20:20 NAMD_D2_sample.dcd
 78M Feb 29 20:20 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.