EBI InterPro MCP Server for Pydantic AIGive Pydantic AI instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more
GDPR Free for SubscribersPydantic AI brings type-safe agent development to Python with first-class MCP support. Connect EBI InterPro through Vinkius and every tool is automatically validated against Pydantic schemas. catch errors at build time, not in production.
Ask AI about this MCP Server for Pydantic AI
The EBI InterPro MCP Server for Pydantic AI is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Geminiimport asyncio
from pydantic_ai import Agent
from pydantic_ai.mcp import MCPServerHTTP
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
server = MCPServerHTTP(url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")
agent = Agent(
model="openai:gpt-4o",
mcp_servers=[server],
system_prompt=(
"You are an assistant with access to EBI InterPro "
"(16 tools)."
),
)
result = await agent.run(
"What tools are available in EBI InterPro?"
)
print(result.data)
asyncio.run(main())
* 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.
Pydantic AI validates every EBI InterPro tool response against typed schemas, catching data inconsistencies at build time. Connect 16 tools through Vinkius and switch between OpenAI, Anthropic, or Gemini without changing your integration code. full type safety, structured output guarantees, and dependency injection for testable agents.
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 Pydantic AI 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 Pydantic AI
When Pydantic AI 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 Pydantic AI via MCP
Follow these steps to wire EBI InterPro into Pydantic AI. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install Pydantic AI
pip install pydantic-aiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
agent.py and run: python agent.pyExplore tools
Why Use Pydantic AI with the EBI InterPro MCP Server
Pydantic AI provides unique advantages when paired with EBI InterPro through the Model Context Protocol.
Full type safety: every MCP tool response is validated against Pydantic models, catching data inconsistencies before they reach your application
Model-agnostic architecture. switch between OpenAI, Anthropic, or Gemini without changing your EBI InterPro integration code
Structured output guarantee: Pydantic AI ensures tool results conform to defined schemas, eliminating runtime type errors
Dependency injection system cleanly separates your EBI InterPro connection logic from agent behavior for testable, maintainable code
EBI InterPro + Pydantic AI Use Cases
Practical scenarios where Pydantic AI combined with the EBI InterPro MCP Server delivers measurable value.
Type-safe data pipelines: query EBI InterPro with guaranteed response schemas, feeding validated data into downstream processing
API orchestration: chain multiple EBI InterPro tool calls with Pydantic validation at each step to ensure data integrity end-to-end
Production monitoring: build validated alert agents that query EBI InterPro and output structured, schema-compliant notifications
Testing and QA: use Pydantic AI's dependency injection to mock EBI InterPro responses and write comprehensive agent tests
Example Prompts for EBI InterPro in Pydantic AI
Ready-to-use prompts you can give your Pydantic AI 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 Pydantic AI
Common issues when connecting EBI InterPro to Pydantic AI through Vinkius, and how to resolve them.
MCPServerHTTP not found
pip install --upgrade pydantic-aiEBI InterPro + Pydantic AI FAQ
Common questions about integrating EBI InterPro MCP Server with Pydantic AI.
How does Pydantic AI discover MCP tools?
MCPServerHTTP instance with the server URL. Pydantic AI connects, discovers all tools, and generates typed Python interfaces automatically.Does Pydantic AI validate MCP tool responses?
Can I switch LLM providers without changing MCP code?
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