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

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.