Bring Interpro
to CrewAI
Learn how to connect EBI InterPro to CrewAI 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 CrewAI?
When paired with CrewAI, EBI InterPro becomes a first-class tool in your multi-agent workflows. Each agent in the crew can call EBI InterPro tools autonomously, one agent queries data, another analyzes results, a third compiles reports, all orchestrated through Vinkius with zero configuration overhead.
- —
Multi-agent collaboration lets you decompose complex workflows into specialized roles, one agent researches, another analyzes, a third generates reports, each with access to MCP tools
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CrewAI's native MCP integration requires zero adapter code: pass Vinkius Edge URL directly in the
mcpsparameter and agents auto-discover every available tool at runtime - —
Built-in task delegation and shared memory mean agents can pass context between steps without manual state management, enabling multi-hop reasoning across tool calls
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Sequential and hierarchical crew patterns map naturally to real-world workflows: enumerate subdomains → analyze DNS history → check WHOIS records → compile findings into actionable reports
EBI InterPro in CrewAI
EBI InterPro and 4,000+ other MCP servers. One platform. One governance layer.
Teams that connect EBI InterPro to CrewAI 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 CrewAI
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 CrewAI 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 CrewAI
Every tool call from CrewAI 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 CrewAI discover and connect to MCP tools?
CrewAI connects to MCP servers lazily. when the crew starts, each agent resolves its MCP URLs and fetches the tool catalog via the standard tools/list method. This means tools are always fresh and reflect the server's current capabilities. No tool schemas need to be hardcoded.
Can different agents in the same crew use different MCP servers?
Yes. Each agent has its own mcps list, so you can assign specific servers to specific roles. For example, a reconnaissance agent might use a domain intelligence server while an analysis agent uses a vulnerability database server.
What happens when an MCP tool call fails during a crew run?
CrewAI wraps tool failures as context for the agent. The LLM receives the error message and can decide to retry with different parameters, fall back to a different tool, or mark the task as partially complete. This resilience is critical for production workflows.
Can CrewAI agents call multiple MCP tools in parallel?
CrewAI agents execute tool calls sequentially within a single reasoning step. However, you can run multiple agents in parallel using process=Process.parallel, each calling different MCP tools concurrently. This is ideal for workflows where separate data sources need to be queried simultaneously.
Can I run CrewAI crews on a schedule (cron)?
Yes. CrewAI crews are standard Python scripts, so you can invoke them via cron, Airflow, Celery, or any task scheduler. The crew.kickoff() method runs synchronously by default, making it straightforward to integrate into existing pipelines.
MCP tools not discovered
Ensure the Edge URL is correct. CrewAI connects lazily when the crew starts. check console output.
Agent not using tools
Make the task description specific. Instead of "do something", say "Use the available tools to list contacts".
Timeout errors
CrewAI has a 10s connection timeout by default. Ensure your network can reach the Edge URL.
Rate limiting or 429 errors
Vinkius enforces per-token rate limits. Check your subscription tier and request quota in the dashboard. Upgrade if you need higher throughput.
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