nf-core/proteinfold Extension

Edit

Extending the existing nf-core/proteinfold pipeline to support protein complex co-folding and structural validation metrics.

Goal

Add three new tools to nf-core/proteinfold to enable co-folding of protein complexes and evaluation of prediction quality — making the pipeline more powerful for drug discovery and structural biology research.

Tasks

1. Add Boltz-2 co-folding module

   Validating Boltz-2 in proteinfold pipeline.

   Level: Intermediate — some Nextflow/nf-core experience recommended.

2. Add US-align structural comparison module

   Write a new nf-core module for usalign/align. US-align measures RMSD and TM-score between a predicted structure and a known reference — quantifying how accurate the prediction is.

   • Source: https://github.com/pylelab/USalign

   Level: Intermediate — some Nextflow/nf-core experience recommended.

3. Add DockQ v2 interface scoring module

   Write new nf-core module for dockq/score. DockQ specifically scores the quality of the binding interface between two proteins

   Issue: https://github.com/nf-core/proteinfold/issues/516

   • Source: https://github.com/bjornwallner/DockQ

   Level: Intermediate — some Nextflow/nf-core experience recommended.

4. Wire new modules into the pipeline

   Connect Boltz-2 → US-align → DockQ into the existing proteinfold workflow and validate with the built-in test profile.

   Issue: https://github.com/nf-core/proteinfold/issues/515

   Level: Intermediate — Nextflow pipeline development experience recommended.