Introduction

This tutorial shows how to transition between two conformational states using adaptive ANM. The example used in this tutorial is the GroEL chaperonin in the R’’ and T states (chain A of PDB structures 1GRU and 1GR5), which we previously studied using this method (see Figure 4 of [ZY09]).

Required Programs

The latest version of ProDy is required.

Getting Started

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

First, we will make necessary imports from ProDy and other 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.

[ZY09]

Yang Z, Májek P, Bahar I. Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. PLoS Comput Biol. 2009 5(4):e1000360.