Bio Structure Annotation
Structure prediction and structure-based annotation.
Instructions
- Run fast embedding screen (tm-vec).
- Predict structures (boltz or colabfold) as needed.
- Search structures with Foldseek and annotate hits.
Quick Reference
| Task | Action |
|---|---|
| Run workflow | Follow the steps in this skill and capture outputs. |
| Validate inputs | Confirm required inputs and reference data exist. |
| Review outputs | Inspect reports and QC gates before proceeding. |
| Tool docs | See docs/README.md. |
| References | - See ../bio-skills-references.md |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor 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.