majiayu000 Bio Structure Annotation
When to use
- Structure prediction and structure-based annotation.
Prerequisites
- Tools installed via pixi (see pixi.toml).
- Reference DB root: /media/shared-expansion/db/ (wsu; override per machine branch).
- Protein FASTA inputs are available.
Inputs
- proteins.faa (FASTA protein sequences)
Outputs
- results/bio-structure-annotation/structures/
- results/bio-structure-annotation/structure_hits.tsv
- results/bio-structure-annotation/structure_report.md
- results/bio-structure-annotation/logs/
Steps
- Run fast embedding screen (tm-vec).
- Predict structures (boltz or colabfold) as needed.
- Search structures with Foldseek and annotate hits.
QC 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.
Validation
- Verify proteins.faa is non-empty and amino acid encoded.
- Verify Foldseek databases exist under the reference root.
Tools
- tm-vec v1.0.3
- boltz v2.2.1
- colabfold v1.5.5
- foldseek v10-941cd33
Paper summaries (2023-2025)
- summaries/ (include example use cases and tool settings used)
Tool documentation
- TM-Vec - Fast protein structure embedding and similarity search
- Boltz - AI-based protein structure prediction
- ColabFold - Fast protein structure prediction using AlphaFold2
- Foldseek - Fast structure-based protein search
References
- See ../bio-skills-references.md