Rafael Brent

Currently we do not have support for nanobody or antibody design with RFD3, as it requires 2d distance conditioning to specify the internal structures of the framework/target without giving the...

Did you use an inverse folding tool such as ProteinMPNN? At present, the sequences designed by RFD3 are unlikely to pass refolding filters, so we recommend using an auxiliary sequence...

Thanks for the detailed information! Those MPNN settings look reasonable. When running AF3, what settings did you use for MSAs/templating? I would recommend to not use MSAs and to use...

Thanks for flagging this. We looked into it further and it is because in our default settings, we had unintentionally been setting `is_non_loopy` to True. We think this is especially...