search

KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
216 stars 48 forks source link

Running a oligomer with a monomer together #210

Closed RenhaoL closed 8 months ago

RenhaoL commented 11 months ago

Hi there,

I want to run Alphafold on a protein against a dimer receptor. I have one sequence for the protein and one sequence for the monomer of the receptor. I was wondering which model I could achieve this. I tried to use the homo-oligomer mode and specified the PDB number in the state file as 2L34_1,2;8AVB_1 (I need 2L34_1 to be a dimer and 8AVB_1 to be monomer in the same system), but I got errors. Any advice is appreciated.

Thanks in advance,

dingquanyu commented 11 months ago

Hi,

Thanks a lot for your interest in our package. Certainly AlphaPulldown is able to facilitate this type of modelling. I would suggest using custom mode instead and in the input instruction, you could write 2L34_1;2L34_1;8AVB_1 so that you will have the 2L34_1 homodimer. Hope it helps.

Yours Dingquan

dingquanyu commented 8 months ago

Hi @RenhaoL

Just checking if the issue has been solved?

RenhaoL commented 8 months ago

Yes. Thanks!