Introduction

This tutorial describes sampling alternate protein conformations along Anisotropic Network Model (ANM) modes, then optimizing them using a molecular dynamics program. Conformations obtained in this way can be useful in, for example, docking studies when the target binding site is flexible and can be affected by motions of protein along collective modes.

We will use a structure of mitogen-activated protein kinase 14 (MAPK14), which is also known as p38 MAPK. The structure identifier is 5uoj. PDB and PSF files are provided in documentation files.

Required Programs

Latest version of ProDy, Matplotlib, VMD_ and NAMD are required.

Recommended Programs

IPython is highly recommended for interactive usage.

Getting Started

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

 471 Feb 29  2024 min.conf
437K Feb 29  2024 p38.pdb
1.3M Feb 29  2024 p38.psf

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]: 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.