Introduction

This tutorial shows how to predict and display the interactions within protein structure using the coordinates (single PDB) or ensemble of conformations (multi-model PDB or dcd file gerenarted by NAMD_ program).

This module can be successfully used to study the distribution of different types of interactions (hydrogen bonds, salt bridges, repulsive ionic binding, pi-cation, pi-stacking, hydrophobic interactions, and disulfide bonds) within protein structure. It may help to distinguish the difference between wild type protein and its mutant, indentify regions or simply residues which are privileged to create a larger number of potential interactions in single PDB, ensemble PDB (NMR data) or during the molecular dynamics simulation.

Required Programs

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.

To take full advantage of InSty’s capabilities in predicting hydrophobic interactions, we should download an additional component written in C++ and Fortran. The additional component (hpb.so file) is available in the ProDy repository (prody/proteins/hpbmodule folder) and should be chosen and selected according to the version of Python that is being used by user. This file should be copied to the ProDy folder (prody/proteins/) or to the local directory.

Moreover, in the case of the lack of hydrogen atoms in protein structure, additional package such as Openbabel or PDBfixer are required for predicting hydrogen bonds.

Getting Started

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

1.5M Feb 29 20:20 5kqm_all_sci.pdb
222K Feb 29 20:20 addH_5kqm.pdb
3.3M Feb 29 20:20 addH_7laf.pdb
4.5M Feb 29 20:20 NAMD_D2_co100.dcd

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

In [4]: ion()

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