How to Use the UniProt MCP in LangChain

Q: How do I search for a specific UniProt ID using LangChain?

Use getuniprotprotein and provide the accession ID. The agent executes this first, giving you immediate access to that protein's full record.

Q: Can I find all isoforms for a gene using UniProt and LangChain?

Yes. searchuniprotgene gathers every isoform linked to that specific gene, along with their individual functional notes. This is perfect for comprehensive structural analysis.

Q: Does the MCP Server support searching by common protein names in LangChain?

Absolutely. The searchuniprot tool lets you use well-known identifiers like 'insulin' or 'hemoglobin' to kick off a search across the 250M+ database.

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Connect UniProt MCP to LangChain

Create your Vinkius account to connect UniProt to LangChain and route execution through our secure gateway. The platform manages server hosting, runtime updates, and security layers. Configuration requires no manual server provisioning.

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Setup UniProt with LangChain

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Perform precise lookups with the MCP Server.

The `get_uniprot_protein` tool pulls all details for a given UniProt accession ID. You pass in an ID, and it returns the complete record—everything from sequence data to functional annotations. This direct call lets your agent pinpoint exactly what you need without having to sift through general search results.

Search for proteins across multiple criteria.

Use `search_uniprot` when you don't know the exact ID. You can query by common names, functions, genes (like 'p53'), or even specific protein types like 'spike protein'. The results provide name, gene, organism, function, location, and sequence data. Your agent handles this search step first. Then, it uses the returned list of candidates to decide which secondary tool needs running next.

Find all isoforms using the MCP Server.

The `search_uniprot_gene` function finds proteins associated with a specific gene. It returns every known protein isoform and their unique functional annotations. This is critical when you need to compare variations of one protein. The agent can gather these isoforms first, then feed the list into another tool for comparative analysis.

Setup guide

Set up UniProt MCP in LangChain

Prerequisites

Python 3.10+ installed
langchain-mcp-adapters + langgraph packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run pip install langchain-mcp-adapters langgraph langchain-openai. The MCP adapters package converts MCP tools into native LangChain BaseTool objects.
2

Connect via HTTP transport
Use MultiServerMCPClient with "transport": "http" pointing to your Vinkius endpoint. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Create a ReAct agent
Pass the discovered tools to create_react_agent() from LangGraph. The agent automatically routes UniProt tool calls through the MCP protocol.
4

Run with any LLM
Swap ChatOpenAI for ChatAnthropic, ChatGoogleGenerativeAI, or any LangChain-compatible model. The MCP tools work identically across all providers.

agent.py

from langchain_mcp_adapters.client import MultiServerMCPClient
from langgraph.prebuilt import create_react_agent
from langchain_openai import ChatOpenAI

async with MultiServerMCPClient({
    "uniprot-mcp": {
        "transport": "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,
    )
    result = await agent.ainvoke({
        "messages": "List recent UniProt transactions"
    })
    print(result["messages"][-1].content)

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Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by UniProt. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.

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Common questions about UniProt MCP in LangChain

Use `get_uniprot_protein` and provide the accession ID. The agent executes this first, giving you immediate access to that protein's full record.

The search returns name, gene, organism, function, subcellular location, and sequence. This allows your agent to build a functional profile of the protein based on its role.

Yes. `search_uniprot_gene` gathers every isoform linked to that specific gene, along with their individual functional notes. This is perfect for comprehensive structural analysis.

Absolutely. The `search_uniprot` tool lets you use well-known identifiers like 'insulin' or 'hemoglobin' to kick off a search across the 250M+ database.

This server deals with public protein sequences and functional annotations. Your AI client only processes this non-private biological research data, so there are no user PII concerns.

Use it with your favorite AI tools

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