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@mgiulini
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tutorial about nanobody-antigen modelling using a combination of AI-derived nanobodies and HADDOCK.

The considered case fails with both AlphaFold2 and AlphaFold3.

Missing pieces:

  • link to HADDOCK3 repo examples (will work as soon as added nanobody example data haddock3#1207 gets merged)
  • link to biorxiv preprint (now empty)
  • it would be nice to reference the HADDOCK3 manual when discussing technicalities

Closes #692

@mgiulini mgiulini self-assigned this Feb 21, 2025
@mgiulini mgiulini requested a review from amjjbonvin February 21, 2025 09:16
@AnnaKravchenko
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AnnaKravchenko commented May 20, 2025

Question about BONUS1: do you have similar "native score" in [alascan] compared to the score given by [emscoring]?
Asking because I’ve got delta of 10 - quite a lot - using same workflow (on the different input PDB), so curious if it’s the same in this case

@mgiulini mgiulini merged commit f1b764f into master Jun 25, 2025
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@mgiulini mgiulini deleted the nb-ag-tutorial branch June 25, 2025 08:15
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add nanobody-antigen modelling tutorial

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