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I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below.

enter image description here

Since there are many docking software programs available I would need the easiest to use and dock the proteins as shown above. It would be amazing if the answer could be specific to the proteins which are above specified.

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HADDOCK

HADDOCK is both a web service and a standalone code.

From the web server:

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modelling problems including protein-protein, protein-nucleic acids and protein-ligand.

All the concerns about docking two proteins mentioned here are taking care of by HADDOCK automatically (except the protein resolution).

To register go: https://bianca.science.uu.nl/haddock2.4/

To submit your job: https://bianca.science.uu.nl/haddock2.4/submit/1

To read some tutorials: https://www.bonvinlab.org/education/

Docking software are designed in such a way to allow docking of any protein/ligands. They are not specific for any protein family or type of ligands. As all of them make use of forcefields, the only concern here is about having the right forcefield parameters for all the atoms.

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