bio-protac-degraders
Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.
npx skills add BioTender-max/awesome-bio-agent-skills --skill protac-degraders --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.
## Version Compatibility Reference examples tested with: PRosettaC (web service), DeepTernary 1.0+, AlphaFold3 (constraints-enabled), Boltz-1 / Boltz-2, RDKit 2024.09+, OpenMM 8.1+ (for ternary MD). Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # PROTAC and Bivalent Degrader Design Design bifunctional molecules (PROTACs) that recruit an E3 ubiquitin ligase to a target protein, inducing target ubiquitination and proteasomal degradation. PROTACs differ from traditional drugs: a stable **ternary complex** (target + PROTAC + E3) is required, not just target binding. The PROTAC field exploded post-2020 with clinical successes (ARV-471 estrogen-receptor degrader, ARV-110 androgen-receptor degrader). Postdoc-grade PROTAC design balances **target ligand binding**, **E3 ligand binding**, **linker geometry** (length, rigidity, chemistry), **cooperativity** (positive = ternary stable; negative = hook effect), and **cell per
- Version Compatibility
- E3 Ligase Choice
- Linker Design Principles
- Decision Tree by Scenario
- Ternary Complex Prediction Tools
- Cooperativity (Alpha)
- DC50 / Dmax Characterization
- Ternary Complex Modeling Workflow
- Linker Length Calculation
- Generative Linker Design
- Per-Tool Failure Modes
- PRosettaC -- inaccessible E3 in selected ligase
- DeepTernary -- novel chemotype
- Hook effect at low PROTAC concentration
What does the bio-protac-degraders skill do?
Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill protac-degraders --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.