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ProteinIQ

MCP server

Bioinformatics tools for your AI agent

Connect Claude, Codex, Cursor, or any MCP client to 252+ tools. Your agent picks the method, quotes the cost, runs the job, and reads the results in your workspace.

Get an API keyRead the docs
Terminal
claude mcp add --transport http proteiniq https://proteiniq.io/mcp \
  --header "Authorization: Bearer $PROTEINIQ_API_KEY"

Or use the raw MCP URL

https://proteiniq.io/mcp

Authenticate with a workspace API key as a bearer token.

Ask for the analysis

Describe the research task. The agent picks the tools, checks the cost, and reads the results back.

  • Structure prediction

    Fold this sequence with ESMFold and tell me which regions have low confidence.

    1. get_tool
    2. →quote_job
    3. →submit_job
    4. →get_result

    Submits the job, waits for it to finish, and reads per-residue pLDDT from the saved result.

  • Batch docking

    Dock these 20 SMILES against my receptor with AutoDock Vina. Spend at most 300 credits.

    1. get_tool
    2. →upload_file
    3. →submit_batch
    4. →get_workflow_results

    Runs one batch with a total budget, so further work stops once the limit is reached.

  • Tool selection

    Which tool should I use to predict how this antibody binds its antigen?

    1. list_tools
    2. →get_tool

    Searches the catalog by task and compares inputs, settings, and credit models before suggesting one.

  • Workflows

    Build a workflow that predicts the complex with Boltz-2 and checks it with PoseBusters.

    1. get_workflow_tool
    2. →create_workflow
    3. →validate_workflow

    Drafts and validates the workflow, then saves it for you to review in the web app before it runs.

Questions & answers

Any paid plan. Create a workspace API key and use it as the bearer token. MCP requests share the key's rate limits with the REST API.

Connecting, searching tools, quoting, and reading results are free. Jobs, batches, and workflow runs spend credits as they would in the web app. Each submission carries a spending ceiling, and quote_job prices the input before anything runs.

Yes. The API key's scopes decide what an agent can read, write, and run, for example read access to results without permission to submit work. Every job it runs appears in your workspace with its inputs, settings, and files.

Any client that supports streamable HTTP with custom headers, including Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI. Claude Desktop connects through the mcp-remote bridge.

It can upload and read files, organize work into projects, submit batches, and create, validate, publish, and run workflows. The MCP reference lists every action.

Use MCP when an agent should choose and run analyses in conversation. Use the REST API or Python SDK when your own code owns the orchestration.

ProteinIQ

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