I found a structure of a binary protein complex and tried to use it as my template to predict the combined structure of another 2 proteins. In this case, should I use the protein-protein docking protocol or the comparative modeling protocol? If I should use the protein-protein docking protocol, is there anyway for me to utilize the PDB file of the template structure to save me some work? And if I should use comparative modeling, how can I build a structure by inputting 2 queries? I assumed that homology modeling only deals with one input query?
Thanks a lot for any clarification.
this is a little confusing to me, but if you have a binary protein complex, you can separate them into two files, one for each protein, do a sequence-alignment and then thread your sequence (change the template protein's sequence to your target sequence) on to your respective template proteins using the partial_thread app in rosetta.
following the tutorials at http://www.meilerlab.org/index.php/rosetta-tutorials will probably help you there.
Once you have threading done, you could then combine the structures back together in something like pymol or just a text editor, and use RosettaCM in order to refine the models, giving it both your target sequences as a fasta file with a forwardslash separating the two (it must be in the same order as your pdb file)
Not sure if that makes sense, but that's how I would do it!