Bioinformatics tools for your AI agent
Connect Claude, Codex, Cursor, or any MCP client to 274+ tools. Your agent picks the method, quotes the cost, runs the job, and reads the results in your workspace.
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/mcpAuthenticate 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.
get_toolquote_jobsubmit_jobget_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.
get_toolupload_filesubmit_batchget_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?
list_toolsget_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.
get_workflow_toolcreate_workflowvalidate_workflow
Drafts and validates the workflow, then saves it for you to review in the web app before it runs.
Questions & answers
Every plan, including Free. Clients such as ChatGPT and Claude sign in with OAuth, and jobs use your workspace credits. Connecting with a workspace API key requires a paid plan. Each plan has its own rate limits.
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 scopes you grant to the API key or OAuth connection 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 OAuth sign-in or custom headers, including Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI. ChatGPT connects with OAuth. Claude Desktop connects through the mcp-remote bridge when you use an API key.
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.