Hello, I have two proteins (X and Y); X has 2 chains (A and B), and Y has 1 chain. I want to dock Y with the B chain of X. I don’t understand how to choose the active residues, as the protein structure is not published yet. I predicted the structure, but I have no idea how to choose the active residues. I went through the manual too, but I am still not sure about it. Please help.
Hi there
A few points:
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first you will have to treat your X molecule as a single chain without any residue overlap.
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if you don’t have any information about the binding sites (for both X and Y), best would be to try some ab-initio docking using center of mass restraints and increased sampling (10000 rigidbody models, and 400 for the subsequent steps). This does require guru access.
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you could eventually remove chain A, and at the end filter any model that would overlap with the A-B interface
And as alternative, did you try to run it through Alphafold (2 or 3)?