How to Use the EBI PDBe MCP in CrewAI

Q: Can I use EBI PDBe with CrewAI to find mutant structures?

Yes, the getmutatedresidues tool is specifically designed for this. Your agent can compare the wild-type sequence against the deposited structure to identify engineered mutations.

Deploy specialized agent crews using the EBI PDBe MCP Server for large-scale structural research and automated reporting.

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Connect EBI PDBe MCP to CrewAI

Create your Vinkius account to connect EBI PDBe 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 PDBe with CrewAI

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Perplexity

Role-based structural research

Assign the `search_structures` tool to a researcher agent. It scours the database for specific protein families while a second agent analyzes the results. This division of labor speeds up your data gathering. The researcher finds the PDB IDs, and the analyst agent digs into the specific molecular details.

Inventory molecular components at scale

Utilize `get_molecules` and `get_residue_listing` to build a complete inventory of a protein structure. Your agents process these lists to identify key mutations or modifications. This creates a comprehensive dataset for your analysis. The crew handles the heavy lifting of parsing the raw structural data per chain.

Cross-reference experimental history

Connect agents to `get_publications` to reconcile structural data with original research papers. The crew verifies the methodology and citations before finalizing a report. This ensures your outputs are grounded in peer-reviewed evidence. The agents work sequentially to gather, verify, and document the findings.

Setup guide

Set up EBI PDBe 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 PDBe tools as needed.

crew.py

from crewai import Agent, Task, Crew

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

task = Task(
    description="List recent EBI PDBe 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 PDBe Analyst",
        goal="Access and analyze EBI PDBe data via MCP.",
        backstory="Expert analyst with direct EBI PDBe access.",
        tools=mcp_tools,
    )

    task = Task(
        description="List recent EBI PDBe 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 →

Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by PDBe (Protein Data Bank in Europe). 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 EBI PDBe MCP in CrewAI

You pass the MCP server URL to the agent's tool list. You can filter the tools to restrict each agent to only the functions they need for their role.

CrewAI agents use shared memory to pass context. If one agent retrieves a summary using `get_summary`, the others can access that data to perform further analysis.

You can structure your crew to process entries in batches. By breaking down large tasks, you prevent memory issues and keep the agents focused on manageable data subsets.

Yes, the `get_mutated_residues` tool is specifically designed for this. Your agent can compare the wild-type sequence against the deposited structure to identify engineered mutations.

The server interacts with public PDB coordinates and annotations. Your session is protected by your endpoint token, and no proprietary research data is shared with the EBI database.

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