Question on Binder Design #207
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jamesrgraham
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Hello,
I was testing making a binder to a "random" PDB structure.
The protein is 209aa in length and I chose the hotspot residues and the region within the protein where those residues appear (67-209).
'contigmap.contigs=[A67-209/0 70-100]' 'ppi.hotspot_res=[A68,A79,A183,A195]'
The output contains two chains. 'A' is the poly-gly binder and 'B' appears to be the region from the target protein.
Is the second chain (the target region) simply included for the sake of convenience?
I manually extracted the 'A' chain to add sequence with ProteinMPNN and then made AF structures and am using that to test docking to the original PDB structure.
Is that a reasonable approach?
Thanks!
james
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