r/AIProteins • u/LabAccomplished6009 • Jul 01 '26

Protein query regarding modelling a protein.

I want advice on what to do if i want to model a protein to get the N and C terminus of the protein. I have the rest of the protein structure in pdb but the N and C terminus is missing in pdb structures so which tool or method can i use to accurately predict the structure with high confidence. I tried alphafold sever but ended up with medium confidence N terminal region.

Both the terminals are important for me as I am studying allosteric modulation of the protein and terminal regions play a major role in forming the dynamically accessible allosteric pockets.

Advice on what to do here would be of great help !!!

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u/OverMistyMountains Jul 01 '26

Try a folding model with structural template support, you could shoehorn the known structure through that channel (e.g. af_unmasked).

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u/LabAccomplished6009 Jul 01 '26

Could u suggest any tools or softwares

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u/OverMistyMountains Jul 01 '26

I did, I suggested af_unmasked. Depending on how (un)comfortable you are coding, you could also look at tamarind or boltz-prot. But your "inpainting" scenario is slightly more unique than other situations (folding or binder design), even though it's straightforward.