struct-os DomainOS¶
Status: Scaffold (routing wired, skills pending)
Engine: struct-os
Domain: Protein structure (AlphaFold, RosettaFold, docking, molecular dynamics)
Protein-structure DomainOS: structure prediction (AlphaFold / RosettaFold), docking, molecular dynamics, and binding-pocket analysis. Empty-shell scaffold -- routing is wired with status=scaffold and degrades to the pubmed + chembl MCP fallback until skills are built.
| Field | Value |
|---|---|
| Product | struct-os |
| Engine id | struct-os |
| Intent key | struct_os |
| Repository | Hordago-Labs/struct-os |
| Plugin | struct-os |
| Maturity (registry) | Scaffold (routing wired, skills pending) |
Overview¶
Protein-structure DomainOS: structure prediction (AlphaFold / RosettaFold), docking, molecular dynamics, and binding-pocket analysis. Empty-shell scaffold -- routing is wired with status=scaffold and degrades to the pubmed + chembl MCP fallback until skills are built.
Scientific approach¶
struct-os structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.
| # | Phase | Gate | HITL |
|---|---|---|---|
| 1 | Sequence Prep | Prepare and validate input sequence(s). | No |
| 2 | Structure Prediction | Predict structure (AlphaFold/RosettaFold). | No |
| 3 | Docking | Dock ligands / partners. | No |
| 4 | Molecular Dynamics | Run MD refinement. | No |
| 5 | Binding-Pocket Analysis | Characterize binding pockets. | Yes |
Capabilities & evidence objects¶
Domain tools / skills
alphafoldrosettafolddockingmolecular-dynamics
Evidence objects
| Object | Role | Consumer |
|---|---|---|
result.json |
planned | co-writer |
Canonical artifacts (5-artifact contract)
Planned
The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.
| Artifact | Description |
|---|---|
result.json |
Structured primary result payload for the domain run. |
report.md |
Human-readable narrative summary of the analysis. |
provenance.json |
Tool versions, reference data, and algorithm lineage for reproducibility. |
gate_status.json |
Per-phase gate pass/fail decisions. |
session_summary.json |
Session metadata for replay and audit. |
Standalone quickstart¶
Zero platform dependency
This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).
- Install the standalone
struct-osplugin (Hordago-Labs/struct-os) -- no Hordago platform required. - Invoke the domain skill with a struct-os intent (see the intent keywords below).
- Review the emitted artifacts under the run's output directory.
Intent keywords (route to this engine):
protein structure \bprotein structure\b alphafold docking molecular dynamics rosettafold protein folding structural prediction binding pocket homology model
Worked example¶
AlphaFold structure prediction (planned surface)
A user asks to predict a protein structure and identify a binding pocket. The planned surface prepares the sequence, predicts structure, docks a ligand, and refines with MD. Until skills land, requests degrade to the pubmed + chembl MCP fallback.
Validation & benchmarks¶
Benchmarks
- Planned: CASP-style TM-score / lDDT evaluation
Reproducibility. Planned: provenance.json will pin model weights and MSA database version.
Reference¶
MCP fallback servers (used when the plugin is unavailable): pubmed, chembl
Source documents
- Scaffold-domains ledger (struct-os):
references/scaffold-domains.md
Composition¶
Platform opt-in
struct-os runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.
Cross-domain dependencies
| Engine | Relationship |
|---|---|
aiDevops |
Consumes protein-embedding models produced by MLos. |