I am a beginner in protein-protein interaction studies. I have started using ClusPro 2.0 and would like to know how efficient it is in comparison to Autodoc and other such softwares?
Grammx , Hex and Patchdock are also good. You have to filter out best solution on the basis of Cluster analysis and Experimental data. Autodock is good for small molecule docking.
For blind docking it is the best available docking server, of course a bit of experimental data helps you choose from the multitude of conformations you get as result(for eg. if the interactions you are expecting are they primarily electrostatic etc.). Its utility is further confirmed by recent CASP results.