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Exscientia / abodybuilder3

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Nanobody generation, plddt #11

Open sj584 opened 1 month ago

sj584 commented 1 month ago

Hi, great work! I have questions about this models

  1. I was initially planning to use abodybuilder2 for nanobody structure generation (Nanobodybuilder).

Would it be approapriate for me to use abodybuilder3 for nanobody structure generation compared to Nanobodybuilder in previous version? It seems that this model does not consider nanobody.

  1. abodybuilder2 outputs does not contain plddt score (but error estimates), whereas this model contains plddt in b-factor position. Is that correct?

Thank you in advance for your response.

henrykenlay commented 3 weeks ago

Thanks @sj584!

You are correct, ABB3 was not been trained on nanobodies. I would recommend using NanoBodyBuilder2 from ImmuneBuilder.

ABB3 used pLDDT scores for estimating prediction uncertainty, whereas ImmuneBuilder estimates uncertainty using an ensemble of models (see Section 4 of our manuscript).