What is the difference between Swiss-Prot and TrEMBL entries?

Swiss-Prot contains 570K+ entries that have been manually reviewed and curated by expert biologists — the gold standard for protein annotation. TrEMBL contains 250M+ entries that are computationally annotated from gene sequences. Swiss-Prot entries are marked as 'reviewed' and are highly reliable; TrEMBL entries are automatically generated and may contain errors.

Do I need to register or pay for an API key?

No. UniProt REST API is completely free and open without any authentication. There are no rate limits for reasonable usage patterns. UniProt is funded by the National Institutes of Health (NIH), European Molecular Biology Laboratory (EMBL), and the Swiss Institute of Bioinformatics (SIB).

Can I retrieve full amino acid sequences for proteins?

Yes. Every protein entry includes the full amino acid sequence with length information. The sequence is returned in standard one-letter amino acid code. For very large proteins (10,000+ residues), the sequence may be truncated in the response but the full accession data is always provided for direct download.

UniProt MCP Server for AutoGen 3 tools — connect in under 2 minutes

Name: UniProt
Availability: InStock
Author: Vinkius

microsoft.github.io/autogen/docs/tools/mcp-tools

Built by Vinkius GDPR 3 Tools Framework

Microsoft AutoGen enables multi-agent conversations where agents negotiate, delegate, and execute tasks collaboratively. Add UniProt as an MCP tool provider through Vinkius and every agent in the group can access live data and take action.

Get MCP Server for AI Agents

ASK AI ABOUT THIS MCP SERVER

Open in ChatGPT Open in Claude Open in Perplexity

Vinkius supports streamable HTTP and SSE.

python

import asyncio
from autogen_agentchat.agents import AssistantAgent
from autogen_ext.tools.mcp import McpWorkbench

async def main():
    # Your Vinkius token. get it at cloud.vinkius.com
    async with McpWorkbench(
        server_params={"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"},
        transport="streamable_http",
    ) as workbench:
        tools = await workbench.list_tools()
        agent = AssistantAgent(
            name="uniprot_agent",
            tools=tools,
            system_message=(
                "You help users with UniProt. "
                "3 tools available."
            ),
        )
        print(f"Agent ready with {len(tools)} tools")

asyncio.run(main())

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About UniProt MCP Server

Connect your AI agent to UniProt — the Universal Protein Resource — the world's definitive knowledge base for protein sequence and functional information.

AutoGen enables multi-agent conversations where agents negotiate, delegate, and collaboratively use UniProt tools. Connect 3 tools through Vinkius and assign role-based access. a data analyst queries while a reviewer validates, with optional human-in-the-loop approval for sensitive operations.

What you can do

Protein Search — Find proteins by name, gene symbol, function, or organism across 250M+ entries from both TrEMBL (auto-annotated) and Swiss-Prot (manually curated)
Accession Lookup — Get complete protein data by UniProt accession number (e.g., P04637 for human p53) including function, subcellular location, and full amino acid sequence
Gene Search — Find all proteins encoded by a specific gene name across multiple organisms to compare orthologs and paralogs

The UniProt MCP Server exposes 3 tools through the Vinkius. Connect it to AutoGen in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

How to Connect UniProt to AutoGen via MCP

Follow these steps to integrate the UniProt MCP Server with AutoGen.

Install AutoGen

Run pip install "autogen-ext[mcp]"

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token

Integrate into workflow

Use the agent in your AutoGen multi-agent orchestration

Explore tools

The workbench discovers 3 tools from UniProt automatically

Why Use AutoGen with the UniProt MCP Server

AutoGen provides unique advantages when paired with UniProt through the Model Context Protocol.

Multi-agent conversations: multiple AutoGen agents discuss, delegate, and collaboratively use UniProt tools to solve complex tasks

Role-based architecture lets you assign UniProt tool access to specific agents. a data analyst queries while a reviewer validates

Human-in-the-loop support: agents can pause for human approval before executing sensitive UniProt tool calls

Code execution sandbox: AutoGen agents can write and run code that processes UniProt tool responses in an isolated environment

UniProt + AutoGen Use Cases

Practical scenarios where AutoGen combined with the UniProt MCP Server delivers measurable value.

Collaborative analysis: one agent queries UniProt while another validates results and a third generates the final report

Automated review pipelines: a researcher agent fetches data from UniProt, a critic agent evaluates quality, and a writer produces the output

Interactive planning: agents negotiate task allocation using UniProt data to make informed decisions about resource distribution

Code generation with live data: an AutoGen coder agent writes scripts that process UniProt responses in a sandboxed execution environment

UniProt MCP Tools for AutoGen (3)

These 3 tools become available when you connect UniProt to AutoGen via MCP:

get_uniprot_protein

Get full protein details by UniProt accession ID

search_uniprot

Returns protein name, gene, organism, function, subcellular location, and sequence. Try: insulin, hemoglobin, p53, BRCA1, spike protein. Search UniProt for proteins by name, function, or keyword

search_uniprot_gene

Returns all protein isoforms and their functional annotations. Find proteins encoded by a specific gene

Example Prompts for UniProt in AutoGen

Ready-to-use prompts you can give your AutoGen agent to start working with UniProt immediately.

"Tell me about the p53 tumor suppressor protein and its function."

"Find all proteins encoded by the BRCA1 gene."

"Look up UniProt accession Q9BYF1 and show me its full details."

Troubleshooting UniProt MCP Server with AutoGen

Common issues when connecting UniProt to AutoGen through the Vinkius, and how to resolve them.

McpWorkbench not found

Install: pip install "autogen-ext[mcp]"

UniProt + AutoGen FAQ

Common questions about integrating UniProt MCP Server with AutoGen.

How does AutoGen connect to MCP servers?

Create an MCP tool adapter and assign it to one or more agents in the group chat. AutoGen agents can then call UniProt tools during their conversation turns.

Can different agents have different MCP tool access?

Yes. AutoGen's role-based architecture lets you assign specific MCP tools to specific agents, so a querying agent has different capabilities than a reviewing agent.