EBI Proteins API MCP Server for Mastra AIGive Mastra AI instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more
GDPR Free for SubscribersMastra AI is a TypeScript-native agent framework built for modern web stacks. Connect EBI Proteins API 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 Proteins API 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-proteins-api": {
url: "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
},
},
});
const tools = await mcpClient.getTools();
const agent = new Agent({
name: "EBI Proteins API Agent",
instructions:
"You help users interact with EBI Proteins API " +
"using 16 tools.",
model: openai("gpt-4o"),
tools,
});
const result = await agent.generate(
"What can I do with EBI Proteins API?"
);
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 Proteins API MCP Server
Connect to the EMBL-EBI Proteins API and access comprehensive protein biology data from one of the world's leading bioinformatics institutes.
Mastra's agent abstraction provides a clean separation between LLM logic and EBI Proteins API 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
- Protein Retrieval — Fetch complete protein entries by UniProt accession with names, organisms, gene information, sequences, and cross-references
- Sequence Features — Retrieve annotated domains, binding sites, active sites, signal peptides, transmembrane regions, and disulfide bonds for any protein
- Genetic Variants — Access curated variants from UniProtKB aggregated with large-scale studies including ClinVar, gnomAD, 1000 Genomes, COSMIC, and TOPMed
- Proteomics & PTMs — Query mass-spectrometry peptide evidence and post-translational modifications from PeptideAtlas, MaxQB, EPD, and ProteomicsDB
- Mutagenesis — Explore curated mutagenesis experiments with detailed phenotypic effect descriptions
- Proteomes & Taxonomy — Search reference proteomes and navigate the taxonomy tree by ID or organism name
- Genome Coordinates — Map proteins to genome positions on GRCh38/GRCh37 with Ensembl gene, transcript, and translation IDs
The EBI Proteins API 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 Proteins API tools available for Mastra AI
When Mastra AI connects to EBI Proteins API through Vinkius, your AI agent gets direct access to every tool listed below — spanning proteins, uniprot, bioinformatics, 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 antigen on EBI Proteins API
These are peptide regions used for antibody generation, indicating experimentally validated protein expression targets. Useful for immunology and antibody-based research. Get antigen sequences from Human Protein Atlas
Get coordinates on EBI Proteins API
Returns Ensembl gene, transcript, and translation IDs along with chromosome, start/end positions, and strand information. Essential for bridging protein annotations with genomic data. Get genome coordinate mappings for a protein
Get genecentric on EBI Proteins API
Shows canonical protein and related protein count for each gene. Use with a UniProt Proteome ID (e.g. UP000005640). Get the gene-centric view of a proteome
Get mutagenesis on EBI Proteins API
Each entry includes the wild-type and mutant residues, position, and a description of the functional impact. Critical for understanding structure-function relationships. Get mutagenesis experiments and phenotypic effects
Get protein on EBI Proteins API
Use a UniProt accession such as P12345, Q9Y6K9, or P53_HUMAN. Retrieve a full protein entry by UniProt accession
Get protein features on EBI Proteins API
Features include domains, binding sites, active sites, signal peptides, transmembrane regions, disulfide bonds, glycosylation sites, and more. Each feature has start/end positions and evidence counts. Get sequence feature annotations for a protein
Get proteome on EBI Proteins API
Returns taxonomy, protein count, gene count, reference status, and component information. Use IDs like UP000005640 for human proteome or UP000000589 for mouse. Get a specific proteome by UniProt Proteome ID
Get proteomics on EBI Proteins API
Shows which peptides have been experimentally detected and whether they are unique to this protein. Essential for validating protein expression. Get mass-spectrometry proteomics data for a protein
Get proteomics ptm on EBI Proteins API
Provides residue-level PTM positions with evidence counts. Get post-translational modifications from mass-spec data
Get taxonomy on EBI Proteins API
Returns scientific name, common name, rank, lineage, parent, and children nodes. Use IDs like 9606 for human, 10090 for mouse, 562 for E. coli. Get taxonomy node details by NCBI taxon ID
Get variation on EBI Proteins API
Each variant includes wild-type and mutant residues, clinical significance, consequence type (e.g. missense, nonsense), and cross-references. Critical for clinical genomics and variant interpretation. Get genetic variants for a protein from multiple sources
Search features by type on EBI Proteins API
Valid types include: DOMAIN, BINDING, ACTIVE_SITE, SIGNAL, TRANSMEM, DISULFID, CARBOHYD, MOD_RES, VARIANT, MUTAGEN, REGION, MOTIF, SITE, REPEAT, COILED, COMPBIAS, HELIX, STRAND, TURN. Search features by type across proteins
Search proteins on EBI Proteins API
You can combine gene name (e.g. TP53), organism (e.g. human, 9606), keyword (e.g. kinase), or accession. Returns a summarized list of matching proteins with names, organisms, and sequence lengths. Search proteins by gene name, organism, or keyword
Search proteomes on EBI Proteins API
Returns proteome IDs, taxonomy, protein counts, gene counts, and reference proteome status. Use queries like "homo sapiens", "escherichia coli", "arabidopsis". Search proteomes by organism name
Search taxonomy on EBI Proteins API
Returns matching taxonomy entries with scientific names, common names, taxon IDs, and ranks. Useful for finding the correct taxon ID before querying proteins or proteomes for a specific organism. Search taxonomy by organism name
Search variation on EBI Proteins API
g. large_scale_study, uniprot, mixed), consequence type (e.g. missense, stop gained), and wild-type residue. Use this to find clinically relevant variants across the proteome. Search variants by consequence type, source, or residue
Connect EBI Proteins API to Mastra AI via MCP
Follow these steps to wire EBI Proteins API 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 Proteins API MCP Server
Mastra AI provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.
Mastra's agent abstraction provides a clean separation between LLM logic and tool infrastructure. add EBI Proteins API 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 Proteins API 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 Proteins API + Mastra AI Use Cases
Practical scenarios where Mastra AI combined with the EBI Proteins API MCP Server delivers measurable value.
Automated workflows: build multi-step agents that query EBI Proteins API, process results, and trigger downstream actions in a typed pipeline
SaaS integrations: embed EBI Proteins API 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 Proteins API on a cron and store results in your database automatically
Multi-agent systems: create specialist agents that collaborate using EBI Proteins API tools alongside other MCP servers
Example Prompts for EBI Proteins API in Mastra AI
Ready-to-use prompts you can give your Mastra AI agent to start working with EBI Proteins API immediately.
"Get all known genetic variants for the TP53 tumor suppressor protein."
"Show me the domain architecture and binding sites of the EGFR protein."
"Map the BRCA1 protein to its genome coordinates on GRCh38."
Troubleshooting EBI Proteins API MCP Server with Mastra AI
Common issues when connecting EBI Proteins API to Mastra AI through Vinkius, and how to resolve them.
createMCPClient not exported
npm install @mastra/mcpEBI Proteins API + Mastra AI FAQ
Common questions about integrating EBI Proteins API 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?
Explore More MCP Servers
View all →
ElevenLabs
10 toolsGenerate high-quality AI speech via ElevenLabs — use lifelike voices, manage text-to-speech, track usage, and handle audio dubbing directly from any AI agent.
NVIDIA AI
9 toolsAccess LLMs, embeddings, code generation, and reasoning via NVIDIA API Catalog.
ClinicalTrials.gov
3 toolsSearch the world's largest registry of clinical research studies — covering diseases, drugs, and experimental therapies across all phases.
Tencent CAPTCHA / 腾讯云防水墙
2 toolsTencent's dominant anti-bot and CAPTCHA service — verify tickets and audit risk levels via AI.