tooluniverse-protein-therapeutic-design
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation. Use when asked to design protein binders, therapeutic proteins, or engineer protein function.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-protein-therapeutic-design --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.
# Therapeutic Protein Designer AI-guided de novo protein design using RFdiffusion backbone generation, ProteinMPNN sequence optimization, and structure validation for therapeutic protein development. **KEY PRINCIPLES**: 1. **Structure-first design** - Generate backbone geometry before sequence 2. **Target-guided** - Design binders with target structure in mind 3. **Iterative validation** - Predict structure to validate designs 4. **Developability-aware** - Consider aggregation, immunogenicity, expression 5. **Evidence-graded** - Grade designs by confidence metrics 6. **Actionable output** - Provide sequences ready for experimental testing 7. **English-first queries** - Always use English terms in tool calls (protein names, target names), even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language --- ## When to Use Apply when user asks: - "Design a protein binder for [target]" - "Create a therapeutic protein against [protein/epitope]" - "Design a protein scaffold with [property]" - "Optimize this protein sequence for [function]" - "Design a de novo enzyme for [reaction]" - "Generate protein variants for [target binding
- When to Use
- Critical Workflow Requirements
- 1. Report-First Approach (MANDATORY)
- 2. Design Documentation (MANDATORY)
- Phase 0: Tool Verification
- NVIDIA NIM Tools Required
- Parameter Verification
- Workflow Overview
- Phase 1: Target Characterization
- 1.1 Get Target Structure
- 1.1b EMDB for Membrane Proteins (NEW)
- 1.2 Identify Binding Epitope
- 1.3 Output for Report
- Phase 2: Backbone Generation
What does the tooluniverse-protein-therapeutic-design skill do?
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation. Use when asked to design protein binders, therapeutic proteins, or engineer protein function.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-protein-therapeutic-design --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.