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Proto Bio ships a hosted MCP server, so any MCP-compatible AI agent — Claude Code, Claude Desktop, Cursor, VS Code Copilot, Codex, Gemini — can run Proto’s bioinformatics tools and sequence-optimization runs through natural language. It’s hosted, so there’s nothing to install: point your agent at a URL and authenticate with your Proto API key. Endpoint: https://mcp.evodesign.org/mcp
The server is multi-tenant and holds no key of its own — every request authenticates with the API key in its Authorization header, so your key is never stored on the server.

Connect an agent

Step-by-step setup for Claude Code, Cursor, VS Code, Codex, and Gemini.

Get an API key

Create a key in the Proto dashboard under Settings → API keys (requires a verified email).

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What you can do

Run tools

Discover → inspect → run → fetch: search_tools → get_tool_schema → run_tool → fetch_asset.

Optimize sequences

Design → validate → run → inspect: list_components → validate_program → create_run → get_run_metrics.

Prompts & resources

Prompts surface as slash commands; resources as @-mentions.

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The surface

The full, always-current set of capabilities is defined by the server’s instructions. At a glance:
  • Tools — whoami, list_tools, search_tools, get_tool_schema, get_tool_example, run_tool, fetch_asset, list_components, validate_program, create_run, get_run_status, cancel_run, run_stage, get_run_metrics, get_run_timepoints, get_run_timepoint
  • Prompts — find_tool, tool_walkthrough
  • Resources — proto-tools://tools/{key}, proto-tools://schemas/{key}, proto-tools://citations/{key}, bio://constraints/{key}, bio://generators/{key}, bio://optimizers/{key}

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How it works

Each agent tool call becomes an HTTP request to https://mcp.evodesign.org/mcp carrying your Authorization: Bearer header. The server builds a per-request client scoped to your key, calls the Proto APIs, and returns validated results. There’s no shared state between users, and your key never touches the server’s environment.