Hello
I would like to perform protein-protein docking using HADDOCK webserver, but I do not know what is the interface of these two proteins, and I do not know what are the active residues of them. How can I predict that? Also, when I use WHISCY, it requires to insert alignment file, but I do not have it.
Please guide me through this issue.
In prinsiple, you can start with the literature search - see if there’s any experimental data awaliable. If so, you may not need to make any predictions.
You can also use ARCTIC-3D for an actual prediction.
For WHISCY, you can obtain an aligmenet for you protein using BLAST. Check out this tutorial Structural Bioinformatics & Modelling – Bonvin Lab. The part on homology modelling can help you with the BLAST, the part on docking - with ARCTIC-3D.
And to add some more information, you could run haddock in ab-initio mode, using for example centre-of-mass restraints (does require expert level access).
But HADDOCK is at its best when you can provide some information.
You might also consider using other docking servers for this
Thank you for your guidance.
Thank you. I am experiencing issues with the “ARCTIC-3D” and “WHISCY” webservers. I receive an internal server error when using ARCTIC-3D, and WHISCY does not display any processing or results.
Can you please guide me though this?
What is your input for Arctic3D?
I am only inserting a UniProt ID as an input. Currently it is not giving error, but it is written: No cluster information could be obtained for this job.
this must mean there is no info about interactions from the PDB for this protein
In that case, you can query arctic-3d with a (several) closely related homolog(s) and map back the interacting residues.
An other approach would be to use PeSTo to predict potential interacting residues