EBI Proteins API MCP Server for LangChainGive LangChain instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more
GDPR Free for SubscribersLangChain is the leading Python framework for composable LLM applications. Connect EBI Proteins API through Vinkius and LangChain agents can call every tool natively. combine them with retrievers, memory, and output parsers for sophisticated AI pipelines.
Ask AI about this MCP Server for LangChain
The EBI Proteins API MCP Server for LangChain 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 asyncio
from langchain_mcp_adapters.client import MultiServerMCPClient
from langchain_openai import ChatOpenAI
from langgraph.prebuilt import create_react_agent
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
async with MultiServerMCPClient({
"ebi-proteins-api": {
"transport": "streamable_http",
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
}
}) as client:
tools = client.get_tools()
agent = create_react_agent(
ChatOpenAI(model="gpt-4o"),
tools,
)
response = await agent.ainvoke({
"messages": [{
"role": "user",
"content": "Using EBI Proteins API, show me what tools are available.",
}]
})
print(response["messages"][-1].content)
asyncio.run(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.
LangChain's ecosystem of 500+ components combines seamlessly with EBI Proteins API through native MCP adapters. Connect 16 tools via Vinkius and use ReAct agents, Plan-and-Execute strategies, or custom agent architectures. with LangSmith tracing giving full visibility into every tool call, latency, and token cost.
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 LangChain 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 LangChain
When LangChain 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 LangChain via MCP
Follow these steps to wire EBI Proteins API into LangChain. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install dependencies
pip install langchain langchain-mcp-adapters langgraph langchain-openaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
python agent.pyExplore tools
Why Use LangChain with the EBI Proteins API MCP Server
LangChain provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.
The largest ecosystem of integrations, chains, and agents. combine EBI Proteins API MCP tools with 500+ LangChain components
Agent architecture supports ReAct, Plan-and-Execute, and custom strategies with full MCP tool access at every step
LangSmith tracing gives you complete visibility into tool calls, latencies, and token usage for production debugging
Memory and conversation persistence let agents maintain context across EBI Proteins API queries for multi-turn workflows
EBI Proteins API + LangChain Use Cases
Practical scenarios where LangChain combined with the EBI Proteins API MCP Server delivers measurable value.
RAG with live data: combine EBI Proteins API tool results with vector store retrievals for answers grounded in both real-time and historical data
Autonomous research agents: LangChain agents query EBI Proteins API, synthesize findings, and generate comprehensive research reports
Multi-tool orchestration: chain EBI Proteins API tools with web scrapers, databases, and calculators in a single agent run
Production monitoring: use LangSmith to trace every EBI Proteins API tool call, measure latency, and optimize your agent's performance
Example Prompts for EBI Proteins API in LangChain
Ready-to-use prompts you can give your LangChain 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 LangChain
Common issues when connecting EBI Proteins API to LangChain through Vinkius, and how to resolve them.
MultiServerMCPClient not found
pip install langchain-mcp-adaptersEBI Proteins API + LangChain FAQ
Common questions about integrating EBI Proteins API MCP Server with LangChain.
How does LangChain connect to MCP servers?
langchain-mcp-adapters to create an MCP client. LangChain discovers all tools and wraps them as native LangChain tools compatible with any agent type.Which LangChain agent types work with MCP?
Can I trace MCP tool calls in LangSmith?
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