A professional auditing tool for protein structure prediction and molecular dynamics results to facilitate Go/Hold/Kill decisions in nanovaccine design.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install gate-audit
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install gate-audit using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is Gate Audit for Nanovaccine Computational Design?
The gate-audit skill is a specialized evaluation framework designed for Openclaw Skills users working in computational biology and vaccine development. It synthesizes complex data from structural predictions (like AlphaFold 3 or Boltz-1) and molecular dynamics (MD) simulations to perform rigorous technical audits across four distinct gates. By analyzing structural feasibility, epitope accessibility, and thermodynamic stability, the skill provides a standardized decision-making process for high-stakes research.
This skill ensures that researchers do not move into expensive downstream computations, such as CpHMD or TI-FEP, without meeting strict validation criteria. It acts as a technical gatekeeper, preventing bias by requiring multi-metric validation and checking for common failure modes like broken linkers or inconsistent trajectory repeats.
Gate Audit for Nanovaccine Computational Design Use Cases
- Evaluating structural topology and interface integrity after AF2, AF3, or ESMFold predictions.
- Assessing epitope accessibility and SASA results to ensure dynamic visibility of target regions.
- Reviewing 2-5 ns equilibrium audits to check for system drift or density abnormalities.
- Finalizing 100 ns MD trajectory analysis to compare against historical baselines before escalating to expensive binding free energy calculations.
- Investigating simulation logs and checkpoints for potential errors like "explosions" or missing data.
How Gate Audit for Nanovaccine Computational Design Works
- The user provides raw data or summaries from tools such as AF3, Boltz-1, or MD simulation logs (RMSD, Rg, NPT density).
- The skill performs a Gate 1 Audit to check structural logic, linker conflicts, and topological sanity.
- It executes a Gate 2 Audit focusing on surface accessibility (SASA) and potential conformational collapse.
- A Gate 3 Audit evaluates simulation health, checking for system equilibrium and log file integrity.
- A Gate 4 Audit compares long-term stability against negative controls or baselines.
- The skill synthesizes these findings into a structured report, identifying failure modes and providing a final Go, Hold, or Kill recommendation.
Gate Audit for Nanovaccine Computational Design Setup
To utilize this skill within your environment, ensure your agent has access to the gate-audit definition. You can integrate it into your workflow using the following command structure:
# Example: Triggering a gate audit for a specific MD result
openclaw run gate-audit --data "./path/to/simulation_summary.json"
No additional physical installation is required beyond the Openclaw Skills runtime environment and access to the skill manifest.
Gate Audit for Nanovaccine Computational Design Data Schema & Taxonomy
The skill processes and generates data organized by the following taxonomy:
| Section | Description |
|---|---|
| Input Summary | Overview of provided AF3, SASA, or MD metrics. |
| Gate Determinations | Specific pass/fail status for Gates 1 through 4. |
| Failure Modes | Detailed description of why a structure or simulation failed (e.g., interface error). |
| Decision Metric | Final status: Go (Pass), Hold (Missing data/Uncertain), or Kill (Critical failure). |
| Supplemental Data | List of required re-runs or missing logs needed for a re-audit. |
Gate Audit for Nanovaccine Computational Design Advanced Features
- Multi-Gate Logic: Automatically defaults to 'Hold' if logs are missing or 'Kill' if epitopes are persistently buried.
- Comparative Baseline Support: Evaluates 100 ns trajectories against historical baseline data for consistency.
- Anti-Bias Guardrails: Explicitly prevents the use of a single best trajectory to represent repeated results.
- Tiered Escalation: Determines eligibility for advanced TI-FEP or CpHMD calculations only after all four gates are cleared.
SKILL.md
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