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
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;
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)
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
STRING: functional protein association networks
https://string-db.org
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