I have two proteins that i need to dock. The surface residues involved in interaction for one of the proteins is known from NMR. For the other protein, I need to predict the interaction interface based on a similar previously known protein-protein complex. What software do you recommend me to use for it that would give me an accurate final docking model? thanks for the help
I guess that structural alignment with that protein from similar structure is not reliable in this case?
You can try ZDOCK, but I'd be sceptical about it. But if you know the structure of similar complex you should be able to tell if the results seem legit or not.
http://zdock.umassmed.edu
HEX is a software which is used for protein-protein docking & you can also use DIMPLOT for the analysis of residue-wise interactions between the two macro-molecules.
Best
Rahul Ravichandran
Hi everyone. Thank you all very much for your valuable suggestions, I will try everything that you have suggested and see what works best for my proteins, Thanks again!
Prabha
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