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.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.