How to Use the EBI Proteins API MCP in CrewAI

Q: Can I limit which EBI Proteins API tools a CrewAI agent uses?

Yes, use the toolfilter option in your agent setup. This restricts the agent to only the tools you authorize, maintaining strict control over the crew's actions.

Deploy a crew of autonomous agents to analyze UniProt data and extract functional protein insights using the EBI Proteins API.

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Connect EBI Proteins API MCP to CrewAI

Create your Vinkius account to connect EBI Proteins API to CrewAI 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 EBI Proteins API with CrewAI

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Assign specialized research roles

Give your research agent access to `get_protein_features` while your analyst agent uses `get_variation`. CrewAI separates these concerns into distinct agent roles. Your crew collaborates by sharing memory of the protein entries. This ensures the analyst has the context needed to interpret the researcher's findings.

Monitor proteomics data autonomously

Set a monitor agent to watch for new peptide mappings using `get_proteomics`. When the agent detects a change, it triggers the moderator to act. Your crew operates without you watching. The agents handle the sequential execution of tools to maintain an up-to-date view of the protein expression data.

Filter and refine protein searches

Use `search_features_by_type` to have your crew identify specific domains or binding sites across the entire UniProt knowledge base. Your agents filter these results before presenting you with the final report. This reduces noise and keeps your research focused on relevant protein regions.

Setup guide

Set up EBI Proteins API MCP in CrewAI

Prerequisites

Python 3.10+ installed
crewai package (pip install crewai)
Active Vinkius subscription with a valid endpoint token

1

Install CrewAI
Run pip install crewai to install the framework. MCP support is built-in via the mcps parameter.
2

Add the MCP URL to your agent
Pass your Vinkius endpoint directly to the mcps list. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com. CrewAI handles tool discovery and caching automatically.
3

Kick off your crew
Create a Crew with your agent and tasks. Call crew.kickoff() — the agent will automatically invoke EBI Proteins API tools as needed.

crew.py

from crewai import Agent, Task, Crew

agent = Agent(
    role="EBI Proteins API Analyst",
    goal="Access and analyze EBI Proteins API data via MCP.",
    backstory="Expert analyst with direct EBI Proteins API access.",
    mcps=[
        "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    ],
)

task = Task(
    description="List recent EBI Proteins API transactions",
    agent=agent,
    expected_output="A summary of recent activity",
)

crew = Crew(agents=[agent], tasks=[task])
result = crew.kickoff()
print(result)

Get your connection token →

Prerequisites

Python 3.10+ installed
crewai + crewai-tools packages
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Run pip install crewai crewai-tools. The MCPServerAdapter handles lifecycle management and tool conversion.
2

Connect with MCPServerAdapter
Use MCPServerAdapter as a context manager with SseServerParameters pointing to your Vinkius endpoint. The adapter automatically manages connection lifecycle.
3

Assign tools and run
Pass the returned mcp_tools to your agent's tools parameter. The adapter converts MCP tools to native BaseTool objects compatible with all CrewAI agents.

crew.py

from crewai import Agent, Task, Crew
from crewai_tools import MCPServerAdapter
from mcp import SseServerParameters

server_params = SseServerParameters(
    url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
)

with MCPServerAdapter(server_params) as mcp_tools:
    agent = Agent(
        role="EBI Proteins API Analyst",
        goal="Access and analyze EBI Proteins API data via MCP.",
        backstory="Expert analyst with direct EBI Proteins API access.",
        tools=mcp_tools,
    )

    task = Task(
        description="List recent EBI Proteins API transactions",
        agent=agent,
        expected_output="A summary of recent activity",
    )

    crew = Crew(agents=[agent], tasks=[task])
    result = crew.kickoff()
    print(result)

Get your connection token →

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Common questions about EBI Proteins API MCP in CrewAI

Pass the server URL into the mcps list for each agent. This gives the crew collective access to all 16 protein lookup tools.

Yes, use the tool_filter option in your agent setup. This restricts the agent to only the tools you authorize, maintaining strict control over the crew's actions.

CrewAI agents can share the results of their tool calls. When one agent retrieves a protein entry, the others can access that data in their shared memory space.

Configure the agent to use stdio transport for the server. This allows for direct communication between the agents and the local server process.

The server operates on public UniProt accessions only. It transmits no user-specific biological samples, keeping your research workflow completely private and secure.

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