Bring Interpro
to LlamaIndex
Learn how to connect EBI InterPro to LlamaIndex and start using 16 AI agent tools in minutes. Fully managed, enterprise secure, and ready to use without writing a single line of code.
GDPR Free for SubscribersCompatible with every major AI agent and IDE
Gemini
What is the 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.
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
How it works
- Subscribe to this server
- No API key required — the InterPro API is fully public
- Start classifying proteins from Claude, Cursor, or any MCP-compatible client
Your AI agent becomes a protein domain expert with access to InterPro's unified classification of protein families from 13+ member databases. All data is sourced from the official InterPro REST API maintained by EMBL-EBI.
Who is this for?
- Molecular Biologists — classify unknown proteins into families and predict their functional domains
- Evolutionary Biologists — explore taxonomic distributions of protein domains across the tree of life
- Structural Biologists — find 3D structures containing specific protein domains for comparative analysis
- Bioinformaticians — integrate protein family classifications into automated annotation pipelines
Built-in capabilities (16)
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
Returns clan accession, name, description, and member counts. Use Pfam clan accessions like CL0001. Get Pfam clan (super-family grouping) details
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
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
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
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
Pfam is the most widely used protein domain database. Use accessions like PF00069 (kinase domain), PF00076 (RRM domain). Get Pfam domain or family details
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
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
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
Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations
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
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
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
Returns UniProt accessions, names, lengths, organisms, and annotation counts. Use queries like "insulin", "hemoglobin", "BRCA1". Search proteins in InterPro by name or keyword
Returns taxon IDs, names, ranks, and annotation counts. Use queries like "human", "drosophila", "arabidopsis", "saccharomyces". Search taxonomy by organism name
Why LlamaIndex?
LlamaIndex agents combine EBI InterPro tool responses with indexed documents for comprehensive, grounded answers. Connect 16 tools through Vinkius and query live data alongside vector stores and SQL databases in a single turn. ideal for hybrid search, data enrichment, and analytical workflows.
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Data-first architecture: LlamaIndex agents combine EBI InterPro tool responses with indexed documents for comprehensive, grounded answers
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Query pipeline framework lets you chain EBI InterPro tool calls with transformations, filters, and re-rankers in a typed pipeline
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Multi-source reasoning: agents can query EBI InterPro, a vector store, and a SQL database in a single turn and synthesize results
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Observability integrations show exactly what EBI InterPro tools were called, what data was returned, and how it influenced the final answer
EBI InterPro in LlamaIndex
EBI InterPro and 4,000+ other MCP servers. One platform. One governance layer.
Teams that connect EBI InterPro to LlamaIndex through Vinkius don't need to source, host, or maintain individual MCP servers. Every tool call runs inside a hardened runtime with credential isolation, DLP, and a signed audit chain.
Raw MCP | Vinkius | |
|---|---|---|
| Server catalog | Find and host yourself | 4,000+ managed |
| Infrastructure | Self-hosted | Sandboxed V8 isolates |
| Credential handling | Plaintext in config | Vault + runtime injection |
| Data loss prevention | None | Configurable DLP policies |
| Kill switch | None | Global instant shutdown |
| Financial circuit breakers | None | Per-server limits + alerts |
| Audit trail | None | Ed25519 signed logs |
| SIEM log streaming | None | Splunk, Datadog, Webhook |
| Honeytokens | None | Canary alerts on leak |
| Custom domains | Not applicable | DNS challenge verified |
| GDPR compliance | Manual effort | Automated purge + export |
Why teams choose Vinkius for EBI InterPro in LlamaIndex
The EBI InterPro 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. All 16 tools execute in hardened sandboxes optimized for native MCP execution.
Your AI agents in LlamaIndex only access the data you authorize, with DLP that blocks sensitive information from ever reaching the model, kill switch for instant shutdown, and up to 60% token savings. Enterprise-grade infrastructure, zero maintenance.
* 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
How Vinkius secures
EBI InterPro for LlamaIndex
Every tool call from LlamaIndex to the EBI InterPro MCP Server is protected by DLP redaction, cryptographic audit chains, V8 sandbox isolation, kill switch, and financial circuit breakers.
Frequently asked questions
Do I need an API key?
No. The InterPro API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.
What databases does InterPro integrate?
InterPro integrates 13+ member databases including Pfam (protein families), CDD (conserved domains from NCBI), SMART (signalling domains), Prosite (patterns and profiles), PANTHER (evolutionary classification), Gene3D (structural domains from CATH), HAMAP (microbial families), PRINTS (fingerprints), PIRSF (classification system), SFLD (superfamilies), and NCBIfam. This gives you a unified view of protein domain and family annotations from the world's leading classification resources.
Can I find which organisms have a specific protein domain?
Yes. Use the get_entry_taxonomy tool with any InterPro accession to see the taxonomic distribution of that domain or family. This shows which organisms — from bacteria to humans — contain proteins with that specific domain. It is one of the most powerful tools for evolutionary biology, revealing how protein domains have been conserved or diversified across the tree of life.
How does LlamaIndex connect to MCP servers?
Use the MCP client adapter to create a connection. LlamaIndex discovers all tools and wraps them as query engine tools compatible with any LlamaIndex agent.
Can I combine MCP tools with vector stores?
Yes. LlamaIndex agents can query EBI InterPro tools and vector store indexes in the same turn, combining real-time and embedded data for grounded responses.
Does LlamaIndex support async MCP calls?
Yes. LlamaIndex's async agent framework supports concurrent MCP tool calls for high-throughput data processing pipelines.
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Install: pip install llama-index-tools-mcp
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