Introduction

Release Notes

v2.5.0 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.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Introduction¶

This tutorial shows how to analyze molecular dynamics trajectories, including essential dynamics analysis. This tutorial shows frame-by-frame analysis of trajectories, so it is particularly helpful for analysis of long trajectories that do not fit in your computers memory.

Required Programs¶

Latest versions of ProDy and Matplotlib are required.

Recommended Programs¶

IPython and Scipy are strongly recommended.

Getting Started¶

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

8.4M Feb 29  2024 mdm2.dcd
112K Feb 29  2024 mdm2.pdb
8.4M Feb 29  2024 mdm2sim2.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]: 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.