How to analyze protein - protein docking
Dear All, I am new to bioinformatics. Recently, I generated two protein models via I - TASSER. Subsequently, the two protein models were docked in ClusPro. Now, I am not able to understand how to scan for probable interaction sites based on interface contact residues in SPDB viewer (Deepview). Please help!!!! Any suggestions and help will be highly appreciated! Thank you.
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sanbarb9 •
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You probably need to sit down with a local structural bioinformatics expect to go through your data/results to answer this type of a question. Not being able to look at your data (assuming you have done all the right things) it would be difficult to help via a forum.
I know that ligand docking interaction sites can be plotted in Pymol, but this is a situation where a small ligand is occupying a binding pocket. Then pymol checks the interatomic distances to see the closest polar contacts (<5 Angstroms I think is the threshold). A quick check in SwissProt tells you if your contact residues are previously annotated.
Can this be applied to protein-protein docking? not sure but worth a try if you have alrady docked the protiens.
Thank you very much!