EBI InterPro MCP Server for WindsurfGive Windsurf 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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Windsurf brings agentic AI coding to a purpose-built IDE. Connect EBI InterPro through Vinkius and Cascade will auto-discover every tool. ask questions, generate code, and act on live data without leaving your editor.

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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.

Windsurf's Cascade agent chains multiple EBI InterPro tool calls autonomously. query data, analyze results, and generate code in a single agentic session. Paste Vinkius Edge URL, reload, and all 16 tools are immediately available. Real-time tool feedback appears inline, so you see API responses directly in your 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 Windsurf 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 Windsurf

When Windsurf 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 Windsurf via MCP

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

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"

Add the server

Paste the JSON configuration above into mcp_config.json

Save and reload

Windsurf will detect the new server automatically

Start using EBI InterPro

Open Cascade and ask: "Using EBI InterPro, help me...". 16 tools available

Why Use Windsurf with the EBI InterPro MCP Server

Windsurf provides unique advantages when paired with EBI InterPro through the Model Context Protocol.

Windsurf's Cascade agent autonomously chains multiple tool calls in sequence, solving complex multi-step tasks without manual intervention

Purpose-built for agentic workflows. Cascade understands context across your entire codebase and integrates MCP tools natively

JSON-based configuration means zero code changes: paste a URL, reload, and all 16 tools are immediately available

Real-time tool feedback is displayed inline, so you see API responses directly in your editor without switching contexts

EBI InterPro + Windsurf Use Cases

Practical scenarios where Windsurf combined with the EBI InterPro MCP Server delivers measurable value.

Automated code generation: ask Cascade to fetch data from EBI InterPro and generate models, types, or handlers based on real API responses

Live debugging: query EBI InterPro tools mid-session to inspect production data while debugging without leaving the editor

Documentation generation: pull schema information from EBI InterPro and have Cascade generate comprehensive API docs automatically

Rapid prototyping: combine EBI InterPro data with Cascade's code generation to scaffold entire features in minutes

Example Prompts for EBI InterPro in Windsurf

Ready-to-use prompts you can give your Windsurf 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 Windsurf

Common issues when connecting EBI InterPro to Windsurf through Vinkius, and how to resolve them.

Server not connecting

Check Settings → MCP for the server status. Try toggling it off and on.

EBI InterPro + Windsurf FAQ

Common questions about integrating EBI InterPro MCP Server with Windsurf.

How does Windsurf discover MCP tools?

Windsurf reads the mcp_config.json file on startup and connects to each configured server via Streamable HTTP. Tools are listed in the MCP panel and available to Cascade automatically.

Can Cascade chain multiple MCP tool calls?

Yes. Cascade is an agentic system. it can plan and execute multi-step workflows, calling several tools in sequence to accomplish complex tasks without manual prompting between steps.

Does Windsurf support multiple MCP servers?

Yes. Add as many servers as needed in mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.