Workflow Skills
Workflow skills are guided multi-step pipelines that orchestrate multiple MCP servers via Claude Code. Each skill is a Markdown prompt that Claude follows to execute a complete protein engineering workflow.
Available Workflows
| Skill | Required MCPs | Description |
|---|---|---|
| Fitness Modeling | msa_mcp, plmc_mcp, ev_onehot_mcp, esm_mcp, prottrans_mcp | Protein fitness prediction with multiple ML backbones |
| Binder Design | bindcraft_mcp | De novo binder design using RFdiffusion + ProteinMPNN + AF2 |
| Nanobody Design | boltzgen_mcp | Nanobody CDR loop design with BoltzGen |
How Skills Work
- Install a skill with
pskill install <name>— this auto-installs all required MCPs - Launch Claude Code and invoke the skill as a slash command (e.g.,
/fitness-model) - Claude executes the multi-step pipeline, prompting you for inputs as needed
- Results are saved to a results directory with publication-ready visualizations
Skills are Markdown files installed to .claude/commands/ (slash commands) and .claude/skills/ (Claude Code skills).
Quick Start
# Install a workflow skill
pskill install fitness_modeling
# Launch Claude Code
claude
# Run the skill
> /fitness-model