EBI InterPro MCP Server for CursorGive Cursor instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more

Name: EBI InterPro
Price: 29 USD
Availability: InStock
Rating: 4.9 (1 reviews)
Author: Vinkius

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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.

Ask AI about this MCP Server for Cursor

Open in ChatGPT Open in Claude Open in Perplexity

The EBI InterPro MCP Server for Cursor is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.

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Cursor

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VS Code

JetBrains

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+ other MCP clients

Classic Setup·json

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

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About EBI InterPro MCP Server

Connect to the InterPro API and access the world's most comprehensive resource for protein family, domain, and functional site classification.

Cursor's Agent mode turns EBI InterPro into an in-editor superpower. Ask Cursor to generate code using live data from EBI InterPro and it fetches, processes, and writes. all in a single agentic loop. 16 tools appear alongside file editing and terminal access, creating a unified development environment grounded in real-time information.

What you can do

Domain Classification — Retrieve detailed InterPro entry information including family/domain descriptions, GO terms, and member database cross-references
Multi-Database Access — Query entries from Pfam, CDD, SMART, Prosite, PANTHER, Gene3D, HAMAP, and more through a unified interface
Protein Annotation — Find all InterPro domains, families, and sites annotated on any UniProt protein
Structure Mapping — Discover PDB structures containing proteins that match specific InterPro entries
Taxonomic Distribution — Explore which organisms contain proteins matching a domain or family — essential for evolutionary biology
Proteome Coverage — Assess domain annotation coverage for complete proteomes
Clan Analysis — Navigate Pfam clan hierarchies to understand super-family relationships

The EBI InterPro MCP Server exposes 16 tools through the Vinkius. Connect it to Cursor in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 16 EBI InterPro tools available for Cursor

When Cursor connects to EBI InterPro through Vinkius, your AI agent gets direct access to every tool listed below — spanning interpro, pfam, protein-domains, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

get

Get cdd entry on EBI InterPro

CDD provides curated models for protein domain families and includes additional alignment and structure data. Use accessions like cd00001. Get CDD (Conserved Domain Database) entry details

get

Get clan on EBI InterPro

Returns clan accession, name, description, and member counts. Use Pfam clan accessions like CL0001. Get Pfam clan (super-family grouping) details

get

Get entry on EBI InterPro

Returns name, type (family, domain, homologous superfamily, repeat, site), description, Gene Ontology terms, member database cross-references, and literature count. Use accessions like IPR000001, IPR036291. Get InterPro entry metadata for a family or domain

get

Get entry proteins on EBI InterPro

Returns protein accessions, names, lengths, and source organisms. Useful for finding all members of a protein family across the UniProt database. Get all proteins matching an InterPro entry

get

Get entry structures on EBI InterPro

Returns PDB IDs, names, experiment types, and resolutions. Useful for finding structural representatives of a protein family or domain. Get all PDB structures matching an InterPro entry

get

Get entry taxonomy on EBI InterPro

Returns taxonomy nodes with names, ranks, and protein counts. This answers the evolutionary biology question "which organisms have this domain/family?" and is essential for understanding protein evolution and conservation. Get taxonomic distribution of an InterPro entry

get

Get pfam entry on EBI InterPro

Pfam is the most widely used protein domain database. Use accessions like PF00069 (kinase domain), PF00076 (RRM domain). Get Pfam domain or family details

get

Get protein on EBI InterPro

Returns the protein name, length, source organism, evidence level, fragment status, and counters for how many InterPro entries, Pfam domains, structures, and taxa are associated with it. Get protein details with all domain and family assignments

get

Get protein entries on EBI InterPro

This is the key tool for understanding "what domains does my protein have?" — the fundamental question in protein characterization. Get all InterPro entries matching a specific protein

get

Get proteome on EBI InterPro

Returns proteome ID, organism name, strain, reference status, and counters for associated entries and proteins. Use UniProt proteome IDs like UP000005640 (human). Get proteome details with domain coverage statistics

get

Get structure on EBI InterPro

Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations

get

Get taxonomy on EBI InterPro

Returns the organism name, rank, lineage, number of children taxa, and counters for associated InterPro entries and proteins. Use IDs like 9606 (human), 10090 (mouse), 562 (E. coli). Get taxonomic node with entry and protein counts

list

List entry databases on EBI InterPro

Shows the number of entries in each database. Useful for understanding the scope of available domain and family annotations. List all InterPro member databases and entry counts

Search entries on EBI InterPro

Optionally filter by entry type: family, domain, homologous_superfamily, repeat, or site. Returns accessions, names, types, and protein/structure counts. Use queries like "kinase", "zinc finger", "immunoglobulin". Search InterPro entries by keyword and type

Search proteins on EBI InterPro

Returns UniProt accessions, names, lengths, organisms, and annotation counts. Use queries like "insulin", "hemoglobin", "BRCA1". Search proteins in InterPro by name or keyword

Search taxonomy on EBI InterPro

Returns taxon IDs, names, ranks, and annotation counts. Use queries like "human", "drosophila", "arabidopsis", "saccharomyces". Search taxonomy by organism name

Connect EBI InterPro to Cursor via MCP

Follow these steps to wire EBI InterPro into Cursor. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

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 EBI InterPro

Open Agent mode in chat and ask: "Using EBI InterPro, help me...". 16 tools available

Why Use Cursor with the EBI InterPro MCP Server

Cursor AI Code Editor provides unique advantages when paired with EBI InterPro 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

EBI InterPro + Cursor Use Cases

Practical scenarios where Cursor combined with the EBI InterPro 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

Example Prompts for EBI InterPro in Cursor

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

"What domains and families does the human TP53 protein belong to?"

"Show me all member databases in InterPro and how many entries each has."

"Which organisms have the kinase domain PF00069?"

Troubleshooting EBI InterPro MCP Server with Cursor

Common issues when connecting EBI InterPro to Cursor through 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.

EBI InterPro + Cursor FAQ

Common questions about integrating EBI InterPro 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.