how to do protein-protein interactions?

jwohlwend / boltz

Official repository for the Boltz-1 biomolecular interaction model

MIT License

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how to do protein-protein interactions? #5

Open ricomnl opened 1 week ago

ricomnl commented 1 week ago

hi, from the docs it's currently not clear how to run boltz for two interacting proteins? do you keep the AF2.3MM convention of <protein1>:<protein2> or does one pass them as two separate chains with individually calculated msas? if the latter, where does the MSA pairing happen?

amelie-iska commented 1 week ago

It explains how to set up the YAML or the FASTA here. You just need a new entry for each unique protein.

jwohlwend commented 1 week ago

@amelie-iska is correct! Regarding pairing, I'll be adding a feature for user-defined pairing today or tomorrow, alongside other MSA related updates. For user-defined MSAs without any pairing key (which is what the current code allows but not for long), we default to random pairing. I'll add more documentation on this.