How to Use the EBI Proteins API MCP in Cursor

Q: How do I add the EBI Proteins API MCP Server to Cursor?

Create a .cursor/mcp.json file in your project root and add the server configuration. Once enabled, your agent can immediately call the 16 tools to fetch UniProt data.

Q: Can I use the EBI Proteins API in Cursor to map genomic coordinates?

Yes, your agent calls getcoordinates to retrieve chromosome positions and Ensembl translation IDs. It writes the mapping logic directly into your open source files using real API responses.

Q: Does the EBI Proteins API in Cursor support proteome searches?

Yes, you can search reference proteomes using searchproteomes and retrieve specific details with getproteome. Your agent uses this data to write and test comparative genomics scripts on the fly.

Q: How do I filter protein features by type?

Use searchfeaturesbytype with valid types like DOMAIN or TRANSMEM. The tool returns matching features across proteins, allowing your editor agent to build precise feature maps.

Inject UniProt features, sequence data, and variants directly into your active code files using Cursor.

See Vinkius in Action

Works with every AI agent you already use

…and any MCP-compatible client

MCP Servers - Free for Subscribers

Connect EBI Proteins API MCP to Cursor

Create your Vinkius account to connect EBI Proteins API to Cursor and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

GDPR Free for Subscribers

Setup EBI Proteins API with Cursor

Ask AI about this MCP

ChatGPT

Claude

Perplexity

Inject raw UniProt data directly into Cursor

Write code that interacts with live biological data using `get_protein` and `search_proteins`. Your agent pulls exact sequence lengths and gene names directly into your editor, eliminating the need for placeholder data. This MCP integration allows your workspace to fetch real-time UniProt records during active development. You write parsers and analysis tools against actual live payloads instead of guessing the schema.

Debug variant annotation pipelines with real data

Use `get_variation` and `get_mutagenesis` to test your clinical variant pipelines. The agent pulls active phenotypic effects and clinical significance ratings straight to your Cursor terminal. You can verify how your code handles missense mutations and stop-gained variants without running slow, local database migrations. It makes writing bioinformatic validation scripts significantly faster.

Validate mass-spectrometry peptide mappings

Fetch experimental evidence for protein expression using `get_proteomics` and `get_proteomics_ptm`. Your agent checks whether specific peptides are unique to your target protein right in your coding environment. This workflow replaces manual CSV exports with direct JSON injection. You write your downstream analysis logic while viewing real post-translational modifications.

Setup guide

Set up EBI Proteins API MCP in Cursor

Prerequisites

Cursor installed (macOS, Windows, or Linux)
Active Vinkius subscription with a valid endpoint token

1

Open MCP Settings

Go to Cursor Settings → MCP or open the Command Palette (Cmd+Shift+P / Ctrl+Shift+P) and search for "MCP: Add Server".
2

Add the EBI Proteins API MCP

Cursor will create or open .cursor/mcp.json in your project root. Paste the JSON snippet on the right. Replace [YOUR_TOKEN_HERE] with your endpoint token from cloud.vinkius.com.
3

Enable Agent mode

Open Composer (Cmd+I / Ctrl+I) and switch to Agent mode using the dropdown at the top. MCP tools are only available in Agent mode.
4

Verify the connection

Ask Cursor something like "List my recent EBI Proteins API transactions." If the MCP tools are loaded correctly, Cursor will call the EBI Proteins API tools automatically. You can also check Settings → MCP for a green status indicator.

.cursor/mcp.json

{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

Get your connection token →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by EMBL-EBI Proteins API. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

Why Choose Vinkius

Vinkius connects your tools to AI with real-time monitoring and automatic cost savings — all from one dashboard.

Connect EBI Proteins API now

Real-time monitoring

Live

visibility into every interaction

Connect your favorite tools to your AI and see exactly what's happening — every request, every response, in real time.

Built-in savings

60%

lower AI costs

Vinkius compresses data between your apps and your AI automatically. Lower bills every month — no configuration required.

Single dashboard

One

place for every integration

Every tool your AI connects to, managed from a single screen. One account, complete control.

Common questions about EBI Proteins API MCP in Cursor

Create a `.cursor/mcp.json` file in your project root and add the server configuration. Once enabled, your agent can immediately call the 16 tools to fetch UniProt data.

Yes, your agent calls `get_coordinates` to retrieve chromosome positions and Ensembl translation IDs. It writes the mapping logic directly into your open source files using real API responses.

Yes, you can search reference proteomes using `search_proteomes` and retrieve specific details with `get_proteome`. Your agent uses this data to write and test comparative genomics scripts on the fly.

Use `search_features_by_type` with valid types like DOMAIN or TRANSMEM. The tool returns matching features across proteins, allowing your editor agent to build precise feature maps.

Yes, all queries for variants, sequences, and annotations run in a zero-trust, ephemeral V8 sandbox using our secure MCP protocol. Your proprietary lookup keys and pipeline inputs never persist on the host system.

Use it with your favorite AI tools

Connect this server to Cursor, Claude, VS Code, and more.

OpenAI Agents SDK sdk-python

Google ADK sdk-python

Pydantic AI sdk-python

Vercel AI SDK sdk-typescript