EBI InterPro MCP Server for VS Code CopilotGive VS Code Copilot instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more
GDPR Free for SubscribersGitHub Copilot in VS Code is the most widely adopted AI coding assistant, embedded directly into the world's most popular code editor. With MCP support in Agent mode, Copilot can access external data and APIs to generate context-aware code grounded in real-time information.
Ask AI about this MCP Server for VS Code Copilot
The EBI InterPro MCP Server for VS Code Copilot 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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Gemini{
"mcpServers": {
"ebi-interpro": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
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}
}Vinkius Desktop App
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* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
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.
GitHub Copilot Agent mode brings EBI InterPro data directly into your VS Code workflow. With a project-scoped config, the entire team shares access to 16 tools. Copilot queries live data, generates typed code, and writes tests from actual API responses, all without leaving the editor.
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 VS Code Copilot 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 VS Code Copilot
When VS Code Copilot 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 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 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 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 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 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 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 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 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 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 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 structure on EBI InterPro
Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations
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 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 VS Code Copilot via MCP
Follow these steps to wire EBI InterPro into VS Code Copilot. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Create MCP config
.vscode/mcp.json file in your project rootAdd the server config
Enable Agent mode
Start using EBI InterPro
Why Use VS Code Copilot with the EBI InterPro MCP Server
GitHub Copilot for Visual Studio Code provides unique advantages when paired with EBI InterPro through the Model Context Protocol.
VS Code is used by over 70% of developers. adding MCP tools to Copilot means your team can leverage external data without leaving their primary editor
Project-scoped MCP configs (`.vscode/mcp.json`) let you commit server configurations to your repository, ensuring the entire team shares the same tool access
Copilot's Agent mode integrates MCP tools seamlessly with file editing, terminal commands, and workspace search in a single agentic loop
GitHub's enterprise compliance and audit features extend to MCP tool usage, providing visibility into how AI interacts with external services
EBI InterPro + VS Code Copilot Use Cases
Practical scenarios where VS Code Copilot combined with the EBI InterPro MCP Server delivers measurable value.
Live API integration: Copilot can query an MCP server, inspect the response schema, and generate typed API client code in the same step
DevSecOps workflows: security teams can give developers access to domain intelligence tools directly in their editor for real-time vulnerability assessment during code review
Data pipeline development: Copilot fetches sample data via MCP and generates transformation scripts, validators, and test fixtures from actual API responses
Documentation generation: Copilot queries available tools and auto-generates README sections, API reference docs, and usage examples
Example Prompts for EBI InterPro in VS Code Copilot
Ready-to-use prompts you can give your VS Code Copilot 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 VS Code Copilot
Common issues when connecting EBI InterPro to VS Code Copilot through Vinkius, and how to resolve them.
MCP tools not available
EBI InterPro + VS Code Copilot FAQ
Common questions about integrating EBI InterPro MCP Server with VS Code Copilot.
Which VS Code version supports MCP?
How do I switch to Agent mode?
Can I restrict which MCP tools Copilot can access?
Does MCP work in VS Code Remote or Codespaces?
.vscode/mcp.json work in Remote SSH, WSL, and GitHub Codespaces environments. The MCP connection is established from the remote host, so ensure the server URL is accessible from that environment.Explore More MCP Servers
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