name: bio-structure-annotation description: Structure prediction and structure-based annotation.

Bio Structure Annotation

Structure prediction and structure-based annotation.

Instructions

1. Run fast embedding screen (tm-vec).
2. Predict structures (boltz or colabfold) as needed.
3. Search structures with Foldseek and annotate hits.

Quick Reference

Input Requirements

Prerequisites:

• Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Reference DB root: set BIO_DB_ROOT (default /media/shared-expansion/db/ on WSU).
• Protein FASTA inputs are available. Inputs:
• proteins.faa (FASTA protein sequences)

Output

• results/bio-structure-annotation/structures/
• results/bio-structure-annotation/structure_hits.tsv
• results/bio-structure-annotation/structure_report.md
• results/bio-structure-annotation/logs/

Quality Gates

• Prediction success rate meets project thresholds.
• Search hit thresholds meet project thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• Verify proteins.faa is non-empty and amino acid encoded.
• Verify Foldseek databases exist under the reference root.

Examples

Example 1: Expected input layout

proteins.faa (FASTA protein sequences)

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.