protein-design-qc
Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and publi
npx skills add BioTender-max/awesome-bio-agent-skills --skill protein-design-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Protein Design Quality Control And Ranking **Plain-language role**: Use this skill to decide which designs pass QC and which ones should move forward. ## Critical Limitation **Individual metrics have weak predictive power for binding**. Research shows: - Individual metric ROC AUC: 0.64-0.66 (slightly better than random) - Metrics are **pre-screening filters**, not affinity predictors - **Composite scoring is essential** for meaningful ranking These thresholds filter out poor designs but do NOT predict binding affinity. ## QC Organization QC is organized by **purpose** and **level**: | Purpose | What it assesses | Key metrics | |---------|------------------|-------------| | **Binding** | Interface quality, binding geometry | ipTM, PAE, SC, dG, dSASA | | **Expression** | Manufacturability, solubility | Instability, GRAVY, pI, cysteines | | **Structural** | Fold confidence, consistency | pLDDT, pTM, scRMSD | Each category has two levels: - **Metric-level**: Calculated values with thresholds (pLDDT > 0.85) - **Design-level**: Pattern/motif detection (odd cysteines, NG sites) --- ## Quick Reference: All Thresholds | Category | Metric | Standard | Stringent | Source | |----------|-----
- Critical Limitation
- QC Organization
- Quick Reference: All Thresholds
- Design-Level Checks (Expression)
- Sequential Filtering Pipeline
- Composite Scoring (Required for Ranking)
- Tool-Specific Filtering
- BindCraft Filter Levels
- BoltzGen Filtering
- Design-Level Severity Scoring
- Experimental Correlation
- Campaign Health Assessment
- Failure Recovery Trees
- Too Few Pass pLDDT Filter (< 5% with pLDDT > 0.85)
boltzgen run ... \
What does the protein-design-qc skill do?
Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and publi
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill protein-design-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.