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Protein-Protein Docking or Comparative Modeling

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Protein-Protein Docking or Comparative Modeling

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. 

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Wed, 2020-01-29 19:01

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 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!

Fri, 2020-02-21 18:23