EBI InterPro MCP Server for Mastra AIGive Mastra AI instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more
GDPR Free for SubscribersMastra AI is a TypeScript-native agent framework built for modern web stacks. Connect EBI InterPro through Vinkius and Mastra agents discover all tools automatically. type-safe, streaming-ready, and deployable anywhere Node.js runs.
Ask AI about this MCP Server for Mastra AI
The EBI InterPro MCP Server for Mastra 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 { Agent } from "@mastra/core/agent";
import { createMCPClient } from "@mastra/mcp";
import { openai } from "@ai-sdk/openai";
async function main() {
// Your Vinkius token. get it at cloud.vinkius.com
const mcpClient = await createMCPClient({
servers: {
"ebi-interpro": {
url: "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
},
},
});
const tools = await mcpClient.getTools();
const agent = new Agent({
name: "EBI InterPro Agent",
instructions:
"You help users interact with EBI InterPro " +
"using 16 tools.",
model: openai("gpt-4o"),
tools,
});
const result = await agent.generate(
"What can I do with EBI InterPro?"
);
console.log(result.text);
}
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.
Mastra's agent abstraction provides a clean separation between LLM logic and EBI InterPro tool infrastructure. Connect 16 tools through Vinkius and use Mastra's built-in workflow engine to chain tool calls with conditional logic, retries, and parallel execution. deployable to any Node.js host in one command.
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 Mastra 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 Mastra AI
When Mastra 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 Mastra AI via MCP
Follow these steps to wire EBI InterPro into Mastra AI. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install dependencies
npm install @mastra/core @mastra/mcp @ai-sdk/openaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
agent.ts and run with npx tsx agent.tsExplore tools
Why Use Mastra AI with the EBI InterPro MCP Server
Mastra AI provides unique advantages when paired with EBI InterPro through the Model Context Protocol.
Mastra's agent abstraction provides a clean separation between LLM logic and tool infrastructure. add EBI InterPro without touching business code
Built-in workflow engine chains MCP tool calls with conditional logic, retries, and parallel execution for complex automation
TypeScript-native: full type inference for every EBI InterPro tool response with IDE autocomplete and compile-time checks
One-command deployment to any Node.js host. Vercel, Railway, Fly.io, or your own infrastructure
EBI InterPro + Mastra AI Use Cases
Practical scenarios where Mastra AI combined with the EBI InterPro MCP Server delivers measurable value.
Automated workflows: build multi-step agents that query EBI InterPro, process results, and trigger downstream actions in a typed pipeline
SaaS integrations: embed EBI InterPro as a first-class tool in your product's AI features with Mastra's clean agent API
Background jobs: schedule Mastra agents to query EBI InterPro on a cron and store results in your database automatically
Multi-agent systems: create specialist agents that collaborate using EBI InterPro tools alongside other MCP servers
Example Prompts for EBI InterPro in Mastra AI
Ready-to-use prompts you can give your Mastra 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 Mastra AI
Common issues when connecting EBI InterPro to Mastra AI through Vinkius, and how to resolve them.
createMCPClient not exported
npm install @mastra/mcpEBI InterPro + Mastra AI FAQ
Common questions about integrating EBI InterPro MCP Server with Mastra AI.
How does Mastra AI connect to MCP servers?
MCPClient with the server URL and pass it to your agent. Mastra discovers all tools and makes them available with full TypeScript types.Can Mastra agents use tools from multiple servers?
Does Mastra support workflow orchestration?
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