How to Use the EBI PDBe MCP in AutoGen

Q: How do I register the EBI PDBe MCP server tools with AutoGen agents?

Install autogen-extmcp and use mcpservertools with your Vinkius server URL. Pass the resulting tool list to your AssistantAgent constructor to expose tools like getsummary to the agent.

Q: How do AutoGen agents handle conflicting data from the EBI PDBe MCP Server?

The agents use conversational consensus. If getqualityscores shows poor resolution but getpublications indicates a high-impact paper, the agents debate the trade-offs in their chat log before reaching a decision.

Run multi-agent debates in AutoGen to verify protein assemblies and validate structural quality scores.

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Connect EBI PDBe MCP to AutoGen

Create your Vinkius account to connect EBI PDBe to AutoGen 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 AutoGen

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Debate Structural Quality with AutoGen Agents

`get_quality_scores` retrieves the global validation metrics, including R-factor and resolution, for a PDB entry. In your AutoGen setup, a quality-assurance agent analyzes these metrics to debate whether the structure is reliable enough for docking. A second agent can challenge these findings by calling `get_experiment` to inspect the underlying methodology. This multi-agent conversation ensures you do not import low-resolution structures into your computational workflow.

Resolve Assembly and Ligand Conflicts

`get_assemblies` details the quaternary states, while `get_ligand_monomers` lists all bound small molecules. Your AutoGen agents compare these outputs to determine if a drug candidate binds to a monomer or at an assembly interface. One agent focuses on the biological assembly while another evaluates ligand chemistry. They negotiate and output a consensus report, saving you from manually checking complex crystal structures.

Coordinate Mutation and Sequence Checks via MCP Server

`get_mutated_residues` identifies engineered mutations in the crystallized construct. An AutoGen sequence agent matches these mutations against wild-type data from `get_uniprot_mapping` to flag any functional deviations. The agents coordinate this cross-reference autonomously, passing structural positions back and forth in their chat thread. This collaborative verification ensures your downstream modeling matches the biological target.

Setup guide

Set up EBI PDBe MCP in AutoGen

Prerequisites

Python 3.10+ installed
autogen-ext[mcp] package
Active Vinkius subscription with a valid endpoint token

1

Install AutoGen with MCP
Run pip install "autogen-ext[mcp]" autogen-agentchat. The MCP extension includes mcp_server_tools for stateless tool access.
2

Fetch tools from the MCP
Call mcp_server_tools(SseServerParams(url=...)) with your Vinkius endpoint. Replace [YOUR_TOKEN_HERE] with your token from cloud.vinkius.com.
3

Run your agent
Pass the tools to AssistantAgent and call agent.run(). The agent invokes EBI PDBe tools and returns structured results.

agent.py

from autogen_ext.tools.mcp import SseServerParams, mcp_server_tools
from autogen_agentchat.agents import AssistantAgent
from autogen_ext.models.openai import OpenAIChatCompletionClient

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

tools = await mcp_server_tools(server_params)

agent = AssistantAgent(
    name="EBI PDBe_assistant",
    model_client=OpenAIChatCompletionClient(model="gpt-4o"),
    tools=tools,
)

result = await agent.run("List recent EBI PDBe data")
print(result.messages[-1].content)

Get your connection token →

Prerequisites

Python 3.10+ installed
autogen-ext[mcp] + autogen-agentchat
Active Vinkius subscription with a valid endpoint token

1

Install dependencies
Same packages as above. McpWorkbench is ideal when your agent needs stateful sessions across multiple tool calls.
2

Use McpWorkbench as context manager
Wrap your agent in async with McpWorkbench(...) to maintain shared state and resources. The workbench manages the full MCP session lifecycle.
3

Run with workbench
Pass workbench=workbench to your agent. State is preserved across multiple tool calls within the same session.

agent.py

from autogen_ext.tools.mcp import McpWorkbench, SseServerParams
from autogen_agentchat.agents import AssistantAgent
from autogen_ext.models.openai import OpenAIChatCompletionClient

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

async with McpWorkbench(server_params) as workbench:
    agent = AssistantAgent(
        name="EBI PDBe_assistant",
        model_client=OpenAIChatCompletionClient(model="gpt-4o"),
        workbench=workbench,
    )

    result = await agent.run("List recent EBI PDBe data")
    print(result.messages[-1].content)

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 AutoGen

Install autogen-ext[mcp] and use mcp_server_tools with your Vinkius server URL. Pass the resulting tool list to your AssistantAgent constructor to expose tools like get_summary to the agent.

Yes. The agents share the toolset in their conversation space. One agent can search for structures using search_structures, while another picks up the resulting PDB ID to run get_binding_sites.

The agents use conversational consensus. If get_quality_scores shows poor resolution but get_publications indicates a high-impact paper, the agents debate the trade-offs in their chat log before reaching a decision.

Yes. You connect to the Vinkius managed endpoint using the Streamable HTTP parameters, which the McpToolAdapter automatically translates into the schema format required by AutoGen agents.

Your structural queries, mutated residue lookups, and PDB IDs are sent over an encrypted connection to the EBI PDBe API. Vinkius runs the server in an isolated sandbox, ensuring your research parameters remain confidential.

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