AD
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Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein s…
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数据与复现
PR
protein-qc
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Quality control metrics and filtering thresholds for protein design. 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 biophys….
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/protein-qc
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- designs = designs[designs['pLDDT'] > 0.85]。
- designs = designs[designs['scRMSD'] < 2.0]。
原始文档
SKILL.md 摘录
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 |
|---|---|---|---|---|
| Structural | pLDDT | > 0.85 | > 0.90 | AF2/Chai/Boltz |
| pTM | > 0.70 | > 0.80 | AF2/Chai/Boltz | |
| scRMSD | < 2.0 Å | < 1.5 Å | Design vs pred | |
| Binding | ipTM | > 0.50 | > 0.60 | AF2/Chai/Boltz |
| PAE_interaction | < 12 Å | < 10 Å | AF2/Chai/Boltz | |
| Shape Comp (SC) | > 0.50 | > 0.60 | PyRosetta | |
| interface_dG | < -10 | < -15 | PyRosetta | |
| Expression | Instability | < 40 | < 30 | BioPython |
| GRAVY | < 0.4 | < 0.2 | BioPython | |
| ESM2 PLL | > 0.0 | > 0.2 | ESM2 |
适用场景
- Use protein-qc in 科研工作流 aligned ，支持 this subject area。
- Follow upstream documentation ，用于 full working procedure。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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