HADDOCK, Hex

If you are interesting to identified possible protein-protein networks, I suggest the software STRING (http://string-db.org/). But, if you are interesting in molecular details and modelling a docking software would be better (Autodocking for instance).

Cheers,

Marcelo

ZDOCK

GRAMM

There is a web-based program called PISA that is good if you have a crystal structure of the protein complex.

Ppipred if you have sequences only and haddock to build complex model from structures of components;

I think you can get help from the "STRING" database.

This allow one to view both real and predicted protein:protein interactions based on diverse evidence.

http://func.mshri.on.ca/

Enjoy!

Detection and quantification of protein interactions

http://www.olink.com/products-services/duolink/applications/protein-interactions?gclid=CNzZ_YGU8q0CFUMb6wodqGwLuQ

"Discovery Studio visualizer" free trial version has this facility to find out the interacting residues (H bonds)

Thank you all for valuable suggestions

ROSETTA is a software suite for predicting and designing protein structures,

protein folding mechanisms, and protein-protein interactions.

1. 3Dock Suits

2. Hex and

3. HADDOCK.

But i personally believes that HADDOCK is best for Protein-Protein Docking. Moreover its free!!

Hi, if you want to predict whether a given pair of proteins are interacting, there are some online tools for the prediction:

1. PIPE: http://cgmlab.carleton.ca/PIPE/

2. SPPS: http://mdl.shsmu.edu.cn/SPPS/

In addition to these tools, you can also use SVM to do the job. The kernel functions you can use can be found in the following papers:

1. Predicting protein–protein interactions based only on sequences information

2. Kernel methods for predicting protein–protein interactions

you can also try this: http://dip.doe-mbi.ucla.edu/dip/Main.cgi

Just use accelyrs discovery studio to get better result

STRING: functional protein association networks

https://string-db.org