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Add minibenchmark notebook #15

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6f0e8be
Bump haddock3 to 2026.8.0 and haddock-runner to v4.1.0
Comp-era Aug 28, 2026
e9344b6
Add HADDOCK3 protein-peptide small benchmark notebook
Comp-era Aug 28, 2026
324fd48
Add interactive notebook section to README
Comp-era Aug 28, 2026
4b41e8a
Reword interactive notebook section in README
Comp-era Aug 28, 2026
6121f9c
Simplify README.md for interactive notebook section
Comp-era Aug 28, 2026
94926de
Revise description of notebook workflow
Comp-era Aug 28, 2026
b2a270a
Edit protein-peptide benchmark notebook: fix typos, add 1AWR CAPRI in…
Comp-era Aug 30, 2026
d587c92
Update markdown header for CAPRI results inspection
Comp-era Aug 30, 2026
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6 changes: 6 additions & 0 deletions README.md
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Expand Up @@ -74,6 +74,12 @@ nohup ./run.sh <scenario.yaml> > run.out & disown && tail -f run.out

See [USAGE.md](USAGE.md) for the full guide, SLURM configuration, and troubleshooting.

## Interactive notebook

The [`notebook/HADDOCK3_protein_peptide_small_benchmark.ipynb`](notebook/HADDOCK3_protein_peptide_small_benchmark.ipynb) notebook provides a guided, end-to-end walkthrough of the protein–peptide benchmarking workflow using a small subset of five complexes.

It covers the complete workflow, including software setup, dataset preparation, benchmark execution with `haddock-runner`, HADDOCK3 docking, and analysis.

## Pipeline Overview
```mermaid
%%{init: {'theme': 'default'}}%%
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935 changes: 935 additions & 0 deletions notebook/HADDOCK3_protein_peptide_small_benchmark.ipynb
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@amjjbonvin amjjbonvin Sep 8, 2026

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A few points on the notebook:

  1. Would it work running it directly on a Mac?(I see you are pulling a x86 linux version of the runner)

  2. When referring/describing files (like the config file for the test benchmark), do provide their full path so that users can find them

  3. For rigidbody, the sampling should be ideally a multiple of the number of core for efficiency.

I did run the notebook on colab, the benchmark completed within 5 minutes. Nice! Could not test the EGI notebooks environment because of a current EGI SSO issue.

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4 changes: 2 additions & 2 deletions versions.env
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Expand Up @@ -6,10 +6,10 @@
# > use a commit (must exist on haddocking/haddock3)
# HADDOCK3_VERSION="e5b73f0b102c6c023f07d5ed4d7e8f65c1b2dccb"
# > use pypi version (must exist on pypi)
HADDOCK3_VERSION=2026.7.0
HADDOCK3_VERSION=2026.8.0

# which haddock-runner to be used - github release tag
HADDOCK_RUNNER_TAG=v4.0.0
HADDOCK_RUNNER_TAG=v4.1.0

# which commits of the benchmarks repositories to use

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