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I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; it checks out as the 10 residue chain sits in a known intrinsically disordered region (IDR) of the protein.

I need to find out what structure (⍺-helix, β-sheet, or other) that the MoRF exhibits when the two copies of the protein are bound together via the MoRF.

How would I go about this? Is there any way to do it computationally online?

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I would suggest doing it using ColabFold, the colab implementation of alphafold2. The screenshot from the configuration shows you how to try to predict complex structures.

enter image description here

I'd give the whole sequence of the proteins and not just the fold, in the hopes that the results are more realistic.

Note that it is a computational prediction and not necessarily perfect. It may have difficulty with a disordered region, and it may also be that your region of interest is unstructured even in complex.

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