Summary
Query-conditioned outer product is an update included in MSA Pairformer that allows it to weight homologous sequences differently(1). This was shown to improve weakly conserved inter-protomer contacts in homo-oligomers.
See also
- MSA protein language models can identify intermolecular contacts
- MSA Transformer
- AlphaFold3 inference benefits more from phylogenetically diverse MSAs than deep redundant MSAs
- Sequence-only protein language models implicitly cluster proteins at fineness levels that increase with size
1.
Akiyama Y, Zhang Z, Tang O, Kim RS, Mirdita M, Steinegger M, et al. Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer. Cell. 2026; Available from: https://doi.org/10.1016/j.cell.2026.06.029