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YoshitakaMo / localcolabfold

ColabFold on your local PC
MIT License
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Question: Force to use template with no sequence similarity #250

Open Bienenwolf655 opened 3 months ago

Bienenwolf655 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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