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protein-qc

Maintainer FreedomIntelligence · Last updated April 1, 2026

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….

OpenClawNanoClawAnalysisReproductionprotein-qc🔬 omics & computational biologyprotein structure & designquality

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/protein-qc

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

designs = designs[designs['pLDDT'] > 0.85].
designs = designs[designs['scRMSD'] < 2.0].

Source Doc

Excerpt From SKILL.md

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