Integrate EBI InterPro with Claude, Cursor, Chatbots & AI Agents MCP Server
GDPR Free for SubscribersCompatible with every major AI agent and IDE
GeminiGet 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
Security & Code Integrity Audit
Every tool in the EBI InterPro MCP Server is continuously audited by the Vinkius Security Engine. We guarantee zero-trust payload isolation, strict data boundaries, and deterministic execution for enterprise-grade AI agents.
How Vinkius protects your data
Can I set different limits for each virtual assistant on my team?
Absolutely. You have full control in our command center. You can create an AI agent that only "reads" data so the support team can answer questions, and another superpowered agent that can "edit" and "create" information exclusively for your operations team. Each AI gets exactly the level of access you allow.
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 audit what my AI agents are doing with this integration?
Yes, Vinkius provides an immutable, HMAC-chained audit log. Every tool execution, payload, and response is tracked in real-time on your dashboard, giving you complete visibility into your agent's actions.
Does the AI train on my tools or API data?
No. Vinkius enforces a strict Zero-Retention policy. Your data simply passes through our secure servers to complete the requested action and is instantly forgotten. Nothing you do here is ever stored, logged, or used to train any artificial intelligence.
Supported Use Cases for EBI InterPro
Enable conversational interfaces like ChatGPT and Claude to execute programmatic commands against the EBI InterPro infrastructure.
Connecting interpro with Cursor
Add EBI InterPro to your workspace to support interpro automation. The integration processes the required parameters for the unthinkable execution by LLMs.
Connecting pfam with Cursor
Use the EBI InterPro server to execute pfam operations from your AI agent. The protocol manages state and authentication for continuous the unthinkable workflows.
EBI InterPro. Runs on everything.
From IDE to framework. Every connection governed by Vinkius.
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