What is the difference between Swiss-Prot and TrEMBL entries?

Swiss-Prot contains 570K+ entries that have been manually reviewed and curated by expert biologists — the gold standard for protein annotation. TrEMBL contains 250M+ entries that are computationally annotated from gene sequences. Swiss-Prot entries are marked as 'reviewed' and are highly reliable; TrEMBL entries are automatically generated and may contain errors.

Do I need to register or pay for an API key?

No. UniProt REST API is completely free and open without any authentication. There are no rate limits for reasonable usage patterns. UniProt is funded by the National Institutes of Health (NIH), European Molecular Biology Laboratory (EMBL), and the Swiss Institute of Bioinformatics (SIB).

Can I retrieve full amino acid sequences for proteins?

Yes. Every protein entry includes the full amino acid sequence with length information. The sequence is returned in standard one-letter amino acid code. For very large proteins (10,000+ residues), the sequence may be truncated in the response but the full accession data is always provided for direct download.

UniProt MCP Server for Cursor 3 tools — connect in under 2 minutes

Name: UniProt
Availability: InStock
Author: Vinkius

docs.cursor.com/context/model-context-protocol

Built by Vinkius GDPR 3 Tools IDE

Cursor is an AI-first code editor built on VS Code that integrates LLM-powered coding assistance directly into the development workflow. Its Agent mode enables autonomous multi-step coding tasks, and MCP support lets agents access external data sources and APIs during code generation.

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Classic Setup·json

{
  "mcpServers": {
    "uniprot": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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About UniProt MCP Server

Connect your AI agent to UniProt — the Universal Protein Resource — the world's definitive knowledge base for protein sequence and functional information.

Cursor's Agent mode turns UniProt into an in-editor superpower. Ask Cursor to generate code using live data from UniProt and it fetches, processes, and writes. all in a single agentic loop. 3 tools appear alongside file editing and terminal access, creating a unified development environment grounded in real-time information.

What you can do

Protein Search — Find proteins by name, gene symbol, function, or organism across 250M+ entries from both TrEMBL (auto-annotated) and Swiss-Prot (manually curated)
Accession Lookup — Get complete protein data by UniProt accession number (e.g., P04637 for human p53) including function, subcellular location, and full amino acid sequence
Gene Search — Find all proteins encoded by a specific gene name across multiple organisms to compare orthologs and paralogs

The UniProt MCP Server exposes 3 tools through the Vinkius. Connect it to Cursor in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect UniProt to Cursor via MCP

Follow these steps to integrate the UniProt MCP Server with Cursor.

Open MCP Settings

Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"

Add the server config

Paste the JSON configuration above into the mcp.json file that opens

Save the file

Cursor will automatically detect the new MCP server

Start using UniProt

Open Agent mode in chat and ask: "Using UniProt, help me...". 3 tools available

Why Use Cursor with the UniProt MCP Server

Cursor AI Code Editor provides unique advantages when paired with UniProt through the Model Context Protocol.

Agent mode turns Cursor into an autonomous coding assistant that can read files, run commands, and call MCP tools without switching context

Cursor's Composer feature can generate entire files using real-time data fetched through MCP. no copy-pasting from external dashboards

MCP tools appear alongside built-in tools like file reading and terminal access, creating a unified agentic environment

VS Code extension compatibility means your existing workflow, keybindings, and extensions all work alongside MCP tools

UniProt + Cursor Use Cases

Practical scenarios where Cursor combined with the UniProt MCP Server delivers measurable value.

Code generation with live data: ask Cursor to generate a security report module using live DNS and subdomain data fetched through MCP

Automated documentation: have Cursor query your API's tool schemas and generate TypeScript interfaces or OpenAPI specs automatically

Infrastructure-as-code: Cursor can fetch domain configurations and generate corresponding Terraform or CloudFormation templates

Test scaffolding: ask Cursor to pull real API responses via MCP and generate unit test fixtures from actual data

UniProt MCP Tools for Cursor (3)

These 3 tools become available when you connect UniProt to Cursor via MCP:

get_uniprot_protein

Get full protein details by UniProt accession ID

search_uniprot

Returns protein name, gene, organism, function, subcellular location, and sequence. Try: insulin, hemoglobin, p53, BRCA1, spike protein. Search UniProt for proteins by name, function, or keyword

search_uniprot_gene

Returns all protein isoforms and their functional annotations. Find proteins encoded by a specific gene

Example Prompts for UniProt in Cursor

Ready-to-use prompts you can give your Cursor agent to start working with UniProt immediately.

"Tell me about the p53 tumor suppressor protein and its function."

"Find all proteins encoded by the BRCA1 gene."

"Look up UniProt accession Q9BYF1 and show me its full details."

Troubleshooting UniProt MCP Server with Cursor

Common issues when connecting UniProt to Cursor through the Vinkius, and how to resolve them.

Tools not appearing in Cursor

Ensure you are in Agent mode (not Ask mode). MCP tools only work in Agent mode.

Server shows as disconnected

Check Settings → Features → MCP and verify the server status. Try clicking the refresh button.

UniProt + Cursor FAQ

Common questions about integrating UniProt MCP Server with Cursor.

What is Agent mode and why does it matter for MCP?

Agent mode is Cursor's autonomous execution mode where the AI can perform multi-step tasks: reading files, editing code, running terminal commands, and calling MCP tools. Without Agent mode, Cursor operates in a simpler ask-and-answer mode that doesn't support tool calling. Always ensure you're in Agent mode when working with MCP servers.

Where does Cursor store MCP configuration?

Cursor looks for MCP server configurations in a mcp.json file. You can configure servers at the project level (.cursor/mcp.json in your project root) or globally (~/.cursor/mcp.json). Project-level configs take precedence.

Can Cursor use MCP tools in inline edits?

No. MCP tools are only available in Agent mode through the chat panel. Inline completions and Tab suggestions do not trigger MCP tool calls. This is by design. tool calls require user visibility and approval.

How do I verify MCP tools are loaded?

Open Settings → Features → MCP and look for your server name. A green indicator means the server is connected. You can also check Agent mode's available tools by clicking the tools dropdown in the chat panel.