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Question: Force to use template with no sequence similarity #250

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Bienenwolf655 opened this issue Aug 23, 2024 · 2 comments
Open

Question: Force to use template with no sequence similarity #250

Bienenwolf655 opened this issue Aug 23, 2024 · 2 comments

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@Bienenwolf655
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Hi,

Thanks for the amazing resource! I have backbone structures (from RFdiffusion that consist only of glycin) and I used ProteinMPNN to put a sequence into the backbones. It would be useful to predict the structures of the ProteinMPNN sequences templated by the backbone structures. I tried to circumvent the required sequence similarity to match the template to the query but couldn't find a way around it yet. I would be very appreciative of any recommendations on how to achieve this.

Best,
Sebastian
@Bienenwolf655
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I guess one slightly clumsy way around the issue would be to add the respective sequences to the pdb files but I am trying to avoid that

@YoshitakaMo
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Your question seems outside the scope of AlphaFold/ColabFold's functionality, but how about modifying your pdb files to be all glycines?

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@YoshitakaMo @Bienenwolf655