affinity calculation for antibody-antigen models

Open avilella opened this issue 6 months ago • 1 comments

Is there an ETA for calculating affinities in antibody-antigen queries? What tool would you recommend to calculate affinities for the output of Boltz-2 (cif files) where protein A is a single-chain protein and protein B is a single chain Fv Pair with a linker?

Thx

Jun 10 '25 13:06 avilella

We do not have a timeline to share at this time. I've seen some people have some success using the iPTM with antibodies, but it's not reliable.

Jun 11 '25 04:06 jwohlwend

Thanks for the reply. In a set of mAbs/antigen pairs for which we have experimental positive data, we find higher correlation/anti-correlation between confidence_score than protein_iptm to quantitative factors that we know are important. Is this something that makes sense to you, given the way confidence_score than protein_iptm are calculated for boltz-2 multimer predictions?

Thanks in advance.

Jun 30 '25 11:06 avilella