Specifying Disulphide bonds to AlphaFold

[vineeshsriramoju]

I'm trying to predict the protein structure of an antibody using AlphaFold, but I'm unsure how to specify the disulfide (SS) bonds to AlphaFold. While I can see the disulfide bonds in the Uniprot features, they are not represented in the Fasta sequence. How can I inform AlphaFold about the placement of these disulfide bonds?

[tcoates5]

You can't. The ONLY input that AlphaFold2 takes is the sequence. Most of the time AlphaFold does pretty well at getting the disulfides correct. It does sometimes struggle with having all 4 chains of an antibody at once though, at which point separately modeling segments separated by flexible regions is sometimes much more accurate (in the case of typical antibodies, modeling the fab and fc regions separately)