try any of the commonly used ones. the ones they have on ExPasy are decent.
There is no particular software for these kind of protein-protein interactions available. However, in general the known interactions; e.g. a pathogen protein that is known to bind collagen, fibronectin, host receptors integrins, TLR4 and CD receptors. You can find the homologues of that protein and perform docking and modelling studies by using computer softwares. The best is to select the pathogen surface proteins first and then find their literature their homologues. Then you can prepare the overall known interactions.
Haddock is well known and reliable tool for doing protein protein docking and interactions http://www.nmr.chem.uu.nl/haddock/ rosetta also providing such tools. If u know which protein interacts with host protein of interest than you can go ahead modelling those proteins and try docking using above said tools.
Might Cytoscape apply (http://cytoscape.org/)? It's a network manipulation and visualization tool for data-driven analysis (bottom-up approach), if you meant incorporation of protein-protein interactions derived from literature (and concurrent experiments).
Only protein-protein interaction models are not useful untill you didnt validate them by using functional results, such as site directed mutagenesis, or co-crystallization!
Initially optimise the models in ramachandran plot by using PROCHECK programme, then use CAChe program and do the docking studies for protein-protein interactions and receptor protein interactions. I hope this will help you.....Good Luck.
If you have experiment data(NMR chemical shift perturbation or mutagenesis), you'd better use'Haddock''. Unless try to use servers at Expasy.
HEX is the free software for protein and protein interactions
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