Introduction

Release Notes

v2.0 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Introduction¶

This tutorial shows how to analyze ensembles of experimental structures.

[AB09]

Bakan A, Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A. 2009 106(34):14349-54.

Required Programs¶

Latest version of ProDy and Matplotlib are required.

Recommended Programs¶

IPython and Scipy are recommended for this tutorial.

Getting Started¶

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

There are no required files.

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.