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YoshitakaMo / localcolabfold

ColabFold on your local PC
MIT License
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Question: #187

Open PodevynLoris opened 10 months ago

PodevynLoris commented 10 months ago

Hello, I am new to protein design so this is a noob question , I'll close the issue asap.

I want to predict the complex of a designed monomer (protein 1) and another (protein2) which is an antigen. During the folding , I'd like my monomer(protein1) to mimic the structure of the antibody that original attach to antigen (protein 2).

I have a pdb template (pdb code : 7F62), I also have it locally without the extra molecules.

If I add the --template argument, will my single monomer mimic the structure of the antibody even tho it is made of 2 chains ?

My input : 

>design_spike_complex
FFYLVLGWYEISSGGTYTNYPDTATGRFTISRDNAKNTLYLEMSSLRSEDTAMYYCANFGNSGIISINGQQAAVYVNSGNLSVSSSYLHWYQQKPGSSPKLWIYSTSNLASGNFQGTQIGYGRSPYFISELDVDNNL:PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKXXGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS

Best, Loris

dbolser commented 6 months ago

Try with / without template and see what results you get.

dbolser commented 6 months ago

You could also try --custom-template-path ./your_dir_containing_your_template_pdb_files as described here: https://github.com/YoshitakaMo/localcolabfold/issues/168