Just to complement other colleges answer...

As Mohamed is pointing, there are two main issues:

- If you want to predict the interactions you may perform protein-protein docking, you can use plenty of tools for this purpose. I have used "cluspro" and "rosseta dock" and I am quite happy with the results, although be careful, because different docking programs they may have different docking algorithm implemented that they may be more suitable for one problem or another.

- If you want, to obtain values about the interaction energy, you can use different implementations of the mm-pbsa or mm-gpbsa methods (you can find it in AmberTools, Maestro, Chimera...), or use my tool which actually is quite accurate and fast:

http://ub.cbm.uam.es/software/mmismsa.php

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Javi

There quite a few. Check this: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671387

I like http://pic.mbu.iisc.ernet.in/job.html

If you want to calculate interaction beteween interacting partners, u can perform Docking using Hex,cluspro,haddock. or if u want study the interactions in the complex strcutures?, u can use PDBsum

Just to complement other colleges answer...

As Mohamed is pointing, there are two main issues:

- If you want to predict the interactions you may perform protein-protein docking, you can use plenty of tools for this purpose. I have used "cluspro" and "rosseta dock" and I am quite happy with the results, although be careful, because different docking programs they may have different docking algorithm implemented that they may be more suitable for one problem or another.

- If you want, to obtain values about the interaction energy, you can use different implementations of the mm-pbsa or mm-gpbsa methods (you can find it in AmberTools, Maestro, Chimera...), or use my tool which actually is quite accurate and fast:

http://ub.cbm.uam.es/software/mmismsa.php

--

Javi

I suggest you to use CLUSPRO which is the best tool for docking studies according to the last CAPRI round, and Charmm-gui for calculate the interaction energy.

http://cluspro.bu.edu/login.php

http://www.charmm-gui.org/

A nice bioinformatic suite for protein-protein interactions here.

http://gingraslab.lunenfeld.ca/resources.php?cateName=Software

PrePPI

https://bhapp.c2b2.columbia.edu/PrePPI/

"Predicted interactions are assigned a likelihood using a Bayesian framework that combines structural, functional, evolutionary and expression information. The database contains ~2 million predictions including 31,402 for yeast and 317,813 for human that are considered high confidence based on our analysis. "

STRING and BIND might be useful for study of protein -protein interaction study

Hi Gaurav,

You can try:

http://zdock.umassmed.edu/

I will suggest you try to figure out what kind of algorithms they different servers are using. Since many of them predicts a possible binding positions and 100 or 100+ poses. I will suggest you to perform protein protein docking and then perform a statistical analysis based on these many structures. It will help you to predict the best structure.

thank you all for your nice suggestion..I would like to do some bioinformatics work and want to write down one paper..is it possible to some noble work in protein-protein interaction which i can publish??