---name: antibody-design-agent
description: An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
Best use case
---name: antibody-design-agent is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
description: An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
Teams using ---name: antibody-design-agent should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/antibody-design-agent/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How ---name: antibody-design-agent Compares
| Feature / Agent | ---name: antibody-design-agent | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
description: An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
---name: antibody-design-agent
description: An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
license: MIT
metadata:
author: VUMC / UW Baker Lab
version: "1.0.0"
compatibility:
- system: Python 3.10+
- hardware: GPU required (A100/H100)
allowed-tools:
- run_shell_command
keywords:
- antibody-design
- automation
- biomedical
measurable_outcome: execute task with >95% success rate.
---"
# Antibody Design Agent
This skill brings together cutting-edge tools for antibody engineering, including MAGE (Monoclonal Antibody Generator) and RFdiffusion for Antibodies. It enables the de novo design of antibodies against specific viral or tumoral targets.
## When to Use This Skill
* **De Novo Design**: Generating antibody sequences/structures that bind to a specific antigen.
* **Epitope Targeting**: Designing VHH or binders for a specific epitope on a target protein.
* **Optimization**: Improving the affinity or stability of an existing antibody candidate.
* **Viral Defense**: Rapidly generating antibodies against novel viral strains.
## Core Capabilities
1. **MAGE (Monoclonal Antibody Generator)**: Uses a protein language model to generate diverse antibody sequences against unseen viral strains.
2. **RFdiffusion for Antibodies**: Generates 3D antibody structures that bind to a target structure with high precision.
3. **ProteinMPNN**: Optimizes the sequence of the generated structures for solubility and expression.
## Workflow
1. **Target Definition**: Input the PDB structure or sequence of the antigen (target).
2. **Design Phase**:
* Use **RFdiffusion** to generate the backbone of the binder (CDR loops).
* Use **ProteinMPNN** to design the sequence for the backbone.
* *Alternatively*, use **MAGE** to generate sequences directly from viral strain data.
3. **Validation (In Silico)**: Use AlphaFold3 or ESMFold to predict the complex structure and assess binding confidence (pLDDT, PAE).
4. **Selection**: Rank candidates for synthesis.
## Example Usage
**User**: "Design a VHH nanobody that binds to the RBD of the SARS-CoV-2 KP.2 variant."
**Agent Action**:
1. Retrieves RBD structure for KP.2.
2. Runs `RFdiffusion` with "binder" constraints on the RBD surface.
3. Generates 100 backbone candidates.
4. Sequences them with `ProteinMPNN`.
5. Folds the complexes with `AlphaFold3` to verify binding interface.
6. Returns top 5 sequences.Related Skills
cc-routine-and-class-design
Evaluate routine and class design quality using Code Complete checklists (43 items). Use when designing routines or classes, reviewing class interfaces, choosing between inheritance and containment, or evaluating routine cohesion. Also trigger when tempted to use inheritance as a quick fix under deadline pressure, or when rationalizing 'but it works' for code with deep inheritance or many parameters. Produce severity-tagged reviews (VIOLATION/WARNING/PASS) in CHECKER mode or design decisions in APPLIER mode. Symptoms: vague routine names, >7 parameters, deep inheritance, mixed abstraction levels.
canvas-design
Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create ...
bimverdi-design
Generate BIM Verdi UI components and pages following the established design system. Use when building templates, components, or any frontend for bimverdi.no. Enforces enterprise-calm aesthetics and avoids generic AI patterns.
assertion-design
SystemVerilog Assertions (SVA) as executable specifications. Use when defining timing requirements, protocol specifications, or formal properties for RTL verification.
ascii-ui-designer
Create high-quality ASCII art UI/UX previews for web development with a two-phase approach. Phase 1: Design & Preview - visualize interfaces, explore layouts, refine ideas in ASCII format without code. Phase 2: Implementation - when ready, get HTML/CSS/React code and design tokens. Use for exploring ideas, getting stakeholder feedback, and iterating on design before development.
ascii-design-reviewer
Review Phase 1 ASCII UI designs from a product owner perspective. Analyze user journeys, identify potential issues, ask clarifying questions about requirements and user flows, create Mermaid diagrams (flowcharts, sequence diagrams, state charts), provide detailed system behavior documentation, and document error handling strategies. Use when reviewing ASCII mockups to validate design against actual user needs, understand system workflows, and ensure completeness before moving to implementation.
---name: armored-cart-design-agent
description: AI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.
archetype-designer
Design and manage TraitorSim agent archetypes with OCEAN personality traits, stat biases, and gameplay profiles. Use when creating new archetypes, modifying personality traits, defining character types, or when asked about archetype design, OCEAN traits, Big Five personality, or character templates.
Arcanea Design System
Complete visual design language for Arcanea - cosmic theme tokens, component patterns, animation standards, and Academy-specific aesthetics
apple-ui-design
Apple-inspired clean, minimal, premium UI design. Use when building modern interfaces requiring exceptional UX, clean aesthetics, or Apple-like polish. Triggers on: clean UI, modern design, Apple style, minimal, premium, user-friendly, UX.
apple-hig-designer
Design iOS apps following Apple's Human Interface Guidelines. Generate native components, validate designs, and ensure accessibility compliance for iPhone, iPad, and Apple Watch.
apple-design
Create Apple-inspired modern, minimalist UI designs with glassmorphism, smooth animations, generous whitespace, and elegant typography. Use when designing portfolio websites, landing pages, hero sections, product showcases, or implementing Apple-style components, dark mode, or responsive layouts.