Hi,

NMA is used to identify the rigid regions and the domain flexibility. If you are looking for the two states of protein i.e. in presence or absence of ligand will definitely have different structural flexibility. Depend on the type of protein and the type of binding will tell which will differ from whom and upto what extent.

Here are few articles I will refer to you.

http://dirac.cnrs-orleans.fr/plone/publications/preprints/all-preprints/domain_motions.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279292/

Here are few online servers

http://www.sciences.univ-nantes.fr/elnemo/

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

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

http://molmovdb.org/nma/

I think different visualizer tools could help you.. e.g pymol, spdbv, etc,  Though going through literature would b more precise.

Hi,

NMA is used to identify the rigid regions and the domain flexibility. If you are looking for the two states of protein i.e. in presence or absence of ligand will definitely have different structural flexibility. Depend on the type of protein and the type of binding will tell which will differ from whom and upto what extent.

Here are few articles I will refer to you.

http://dirac.cnrs-orleans.fr/plone/publications/preprints/all-preprints/domain_motions.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279292/

Here are few online servers

http://www.sciences.univ-nantes.fr/elnemo/

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

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

http://molmovdb.org/nma/

I am not sure to understand your question. I see two potions:

- if you assume that the only effect of the ligand is to shift conformational equilibrium and if you have structures that represent the main conformation for the two cases (with/without ligand). then you can use the tool mentioned by Anupam.

- if you have only one conformation and want to see the effect of the ligand on normal modes that is more tricky (see http://www.ncbi.nlm.nih.gov/pubmed/17077146).

I would say yes. Definitely.

You can track changes in flexibility.

BUT: be careful when comparing energies between bound and unbound states. In one case you have a ligand, in the other not. Therefore N, the total number of atoms is different in the two cases so you can't compare energies. If you put your ligand at "infinity" (in practice, this means at a distance from the protein ( > 10Å away at least)) then you can compare energies. Just make sure that N is the same in the two cases.