Please look for following paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836427/

One file is attached

Thank you so much, very good paper with comprehensive reply.

Normal modes will give you large scale flexibility of protein structures. There are many papers reviewing this subject.

It is very fast (when used with a coarse-grained model). "very fast" means seconds or minutes for a large protein in a normal PC.

To get a glimpse of what Normal Model Analysis will tell you, try some servers:

http://lorentz.immstr.pasteur.fr/index1.php

http://mmb.pcb.ub.es/FlexServ/

http://www.igs.cnrs-mrs.fr/elnemo/

http://enm.lobos.nih.gov/

http://apps.cbu.uib.no/webnma/home

http://ignm.ccbb.pitt.edu/

All of them have similar but not equal underlying models.

To better understand these models and work with the data they produce, install a program to calculate normal modes. Here are a couple of suggestions:

http://www.csb.pitt.edu/prody

http://dirac.cnrs-orleans.fr/MMTK/

Hope this helps!

Hi,

Generally the protein motions are classified in to 3800 motions. By using normal mode analysis you can predict most of the structural changes by just perturbing two modes.Many online servers are available to predict normal modes some of them are elnemo,Nomad etc.

http://imods.chaconlab.org/

It's a an online web server.

It's fast. Try it.

Please look at this research paper:

BIo3D package in R will be a good choice generate NMA graph, for interpretations above listed papers, can be used.

Hi, try our method, it typically orders of magnitude faster compared to the other with atom-atom interactions in there,

https://team.inria.fr/nano-d/software/nolb-normal-modes/