EBI Proteins API MCP Server for Pydantic AIGive Pydantic AI instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more

Name: EBI Proteins API
Price: 29 USD
Availability: InStock
Rating: 4.9 (1 reviews)
Author: Vinkius

GDPR Free for Subscribers

Pydantic AI brings type-safe agent development to Python with first-class MCP support. Connect EBI Proteins API through Vinkius and every tool is automatically validated against Pydantic schemas. catch errors at build time, not in production.

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The EBI Proteins API MCP Server for Pydantic AI is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.

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python

import asyncio
from pydantic_ai import Agent
from pydantic_ai.mcp import MCPServerHTTP

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    server = MCPServerHTTP(url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")

    agent = Agent(
        model="openai:gpt-4o",
        mcp_servers=[server],
        system_prompt=(
            "You are an assistant with access to EBI Proteins API "
            "(16 tools)."
        ),
    )

    result = await agent.run(
        "What tools are available in EBI Proteins API?"
    )
    print(result.data)

asyncio.run(main())

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* 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.

Pydantic AI validates every EBI Proteins API tool response against typed schemas, catching data inconsistencies at build time. Connect 16 tools through Vinkius and switch between OpenAI, Anthropic, or Gemini without changing your integration code. full type safety, structured output guarantees, and dependency injection for testable agents.

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 Pydantic 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 Pydantic AI

When Pydantic 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

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

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

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

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

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

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

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

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

Get proteomics ptm on EBI Proteins API

Provides residue-level PTM positions with evidence counts. Get post-translational modifications from mass-spec data

get

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

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 Pydantic AI via MCP

Follow these steps to wire EBI Proteins API into Pydantic AI. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Install Pydantic AI

Run pip install pydantic-ai

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Run the agent

Save to agent.py and run: python agent.py

Explore tools

The agent discovers 16 tools from EBI Proteins API with type-safe schemas

Why Use Pydantic AI with the EBI Proteins API MCP Server

Pydantic AI provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.

Full type safety: every MCP tool response is validated against Pydantic models, catching data inconsistencies before they reach your application

Model-agnostic architecture. switch between OpenAI, Anthropic, or Gemini without changing your EBI Proteins API integration code

Structured output guarantee: Pydantic AI ensures tool results conform to defined schemas, eliminating runtime type errors

Dependency injection system cleanly separates your EBI Proteins API connection logic from agent behavior for testable, maintainable code

EBI Proteins API + Pydantic AI Use Cases

Practical scenarios where Pydantic AI combined with the EBI Proteins API MCP Server delivers measurable value.

Type-safe data pipelines: query EBI Proteins API with guaranteed response schemas, feeding validated data into downstream processing

API orchestration: chain multiple EBI Proteins API tool calls with Pydantic validation at each step to ensure data integrity end-to-end

Production monitoring: build validated alert agents that query EBI Proteins API and output structured, schema-compliant notifications

Testing and QA: use Pydantic AI's dependency injection to mock EBI Proteins API responses and write comprehensive agent tests

Example Prompts for EBI Proteins API in Pydantic AI

Ready-to-use prompts you can give your Pydantic 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 Pydantic AI

Common issues when connecting EBI Proteins API to Pydantic AI through Vinkius, and how to resolve them.

MCPServerHTTP not found

Update: pip install --upgrade pydantic-ai

EBI Proteins API + Pydantic AI FAQ

Common questions about integrating EBI Proteins API MCP Server with Pydantic AI.

How does Pydantic AI discover MCP tools?

Create an MCPServerHTTP instance with the server URL. Pydantic AI connects, discovers all tools, and generates typed Python interfaces automatically.

Does Pydantic AI validate MCP tool responses?

Yes. When you define result types as Pydantic models, every tool response is validated against the schema. Invalid data raises a clear error instead of silently corrupting your pipeline.

Can I switch LLM providers without changing MCP code?

Absolutely. Pydantic AI abstracts the model layer. your EBI Proteins API MCP integration works identically with OpenAI, Anthropic, Google, or any supported provider.

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