I am very new in the field of protein. My question may be funny to you.
Recently through co-ip experiment, I pull down two proteins with gene names:CLPX CPT1A. Now I want to know the residues for them to bind each other. I use Swiss-Model finding their PDB templates. I then use the PDB ID to do the Haddock docking. My HADDOCK run has finished successfully. I got the results. But I don’t know how to interpret the results. I don’t see the residues I am looking for. I am stucked here.
Could you please help me check if my above reasoning make sense or not? Any input is greatly appreciated.
Probably best to start following first some of our online tutorials.
Visit bonvinlab.org/education and check in particular the haddock2.4 tutorials.
In you case you could also try to do some bioinformatics predictions of interfaces to see what you get.
Plenty of software/servers to do that, including our own CPORT and WHISCY servers.
Further you could do a contact analysis of all your models to see if there are “hot spot” regions in your proteins.
Something similar in described in the following small molecule docking tutorial:
And in particular: