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protac-design-agent
Maintainer FreedomIntelligence · Last updated April 1, 2026
PROTAC design: E3 ligase ligand selection, linker optimization, ternary complex modeling.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/protac-design-agent
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- The PROTAC Design Agent provides AI-assisted design of Proteolysis Targeting Chimeras (PROTACs) for targeted protein degradation. It integrates machine learning for ternary complex prediction, linker design, E3 ligase selection, and ADMET optimization to accelerate degrader drug discovery for oncology and other therapeutic areas.
- When designing PROTAC degraders for a target protein.
- For optimizing linker chemistry and length.
- To predict ternary complex formation and degradation efficiency.
- When selecting optimal E3 ligase (CRBN, VHL) for the target.
Source Doc
Excerpt From SKILL.md
Core Capabilities
-
Warhead Selection: Identify optimal target protein ligands.
-
E3 Ligase Selection: Choose CRBN, VHL, or other E3 recruiters.
-
Linker Design: Optimize linker length, chemistry, and rigidity.
-
Ternary Complex Prediction: Model POI-PROTAC-E3 formation.
-
Degradation Efficiency Modeling: Predict DC50 and Dmax.
-
ADMET Optimization: Balance potency with drug-like properties.
PROTAC Components
| Component | Function | Optimization Target |
|---|---|---|
| Warhead | Binds target protein (POI) | Affinity, selectivity |
| E3 Ligand | Recruits E3 ubiquitin ligase | CRBN/VHL binding |
| Linker | Connects warhead to E3 ligand | Length, flexibility, solubility |
E3 Ligase Options
| E3 Ligase | Ligand | Tissue Expression | Advantages |
|---|---|---|---|
| CRBN | Thalidomide analogs | Ubiquitous | Well-characterized |
| VHL | VHL ligands | Ubiquitous | High selectivity |
| MDM2 | Nutlin analogs | Variable | p53-independent |
| IAP | SMAC mimetics | High in cancer | Dual mechanism |
| DCAF15 | Indisulam | Variable | Novel chemistry |
Use cases
- When designing PROTAC degraders for a target protein.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- Molecular_Glue_Discovery_Agent - Glue degraders
- TPD_Ternary_Complex_Agent - Complex prediction
- Molecular_Docking_Agent - Docking analysis
- ADMET_Prediction_Agent - Property prediction
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