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Bonus on interface energetics with prot-on, haddock3-score and alascan #706

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AnnaKravchenko merged 8 commits into from
May 27, 2025
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Bonus on interface energetics with prot-on, haddock3-score and alascan #706

AnnaKravchenko merged 8 commits into from
May 27, 2025

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@AnnaKravchenko AnnaKravchenko commented May 20, 2025 •
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  • Added BONUS 1: Dissecting the interface energetics: how much can a single mutation matter?
  • Renumbered other bonuses, both titles and occurences in the text.

Todo:

  1. Correct interaction-energetics.cfg in zip & update precomputed run :
    Zip archive contains workflow [topoaa]->[emref]->[alascan]. Haddock scores are:
    /1_emref/emref_1.pdb -146.794 but ’native_score’ in [alascan] is -137.3792, which is a big difference.
    It is likely caused by alascan's own refinement. If [emref] is removed from the workflow - the ’native_score’ matches expected score.
  2. Add get-alascan-extrema.sh to ./scripts/
  3. (optional) The alascan part can be extended following example in Nb antiget tutorial: 1. idenfify a possible key residue visually baseed on default alascan output 2. add workflow with all the possible mutations (onther that to Alanine) of selected residue

@AnnaKravchenko AnnaKravchenko linked an issue May 20, 2025 that may be closed by this pull request
add energetic bonus to antibody-antigen tuto #707
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@AnnaKravchenko AnnaKravchenko self-assigned this May 20, 2025
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AnnaKravchenko commented May 20, 2025

Half of the BONUS 1, namely ### PROT-ON and haddock3-scoring to inspect a single mutation is ready for review

amjjbonvin
amjjbonvin approved these changes May 21, 2025
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Nice addition Anna!

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AnnaKravchenko commented May 27, 2025 •
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This bonus is now finised.
New zip added to my surf drive, link to in tuto text updated.
This PR is ready to merge.

--
Conserning summer school: there was a bug in alascan that caused this module to save incorrect models. The bug is fixed, but it is not possible to update summer school participants’ laptops - new haddock3 release is required, etc.

In light of this, I propose to update the last part of the bonus for the duration of the summer school - to hide mutated models and focus on the mutants’ scores only, as this part is functional in current release. And keep a copy of the current verison of the bonus - to rollback when summer school is over.

Does it sound fine, or should I make summer-school-related changes here?

@AnnaKravchenko AnnaKravchenko marked this pull request as ready for review May 27, 2025 11:15
@AnnaKravchenko AnnaKravchenko merged commit ccf738a into master May 27, 2025
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amjjbonvin added a commit that referenced this pull request Jun 6, 2025
@AnnaKravchenko @amjjbonvin
Bonus on interface energetics with prot-on, haddock3-score and alascan (
7dbad30 
#706)

* bonus on interface energetics with prot-on, haddock3-score and alascan

* Update index.md

* add final image

* upd link to zip file

* final round of correcting typos

---------

Co-authored-by: Alexandre Bonvin <[email protected]>
@AnnaKravchenko AnnaKravchenko deleted the antibody-antigen-bonus-energetics branch June 8, 2025 15:57
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add energetic bonus to antibody-antigen tuto

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@AnnaKravchenko @amjjbonvin