EBI PDBe MCP Server for AutoGenGive AutoGen instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersMicrosoft AutoGen enables multi-agent conversations where agents negotiate, delegate, and execute tasks collaboratively. Add EBI PDBe as an MCP tool provider through Vinkius and every agent in the group can access live data and take action.
Ask AI about this MCP Server for AutoGen
The EBI PDBe MCP Server for AutoGen is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Geminiimport 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="ebi_pdbe_agent",
tools=tools,
system_message=(
"You help users with EBI PDBe. "
"16 tools available."
),
)
print(f"Agent ready with {len(tools)} tools")
asyncio.run(main())
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About EBI PDBe MCP Server
Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.
AutoGen enables multi-agent conversations where agents negotiate, delegate, and collaboratively use EBI PDBe tools. Connect 16 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
- Structure Summaries — Get titles, authors, deposition dates, resolution, and experimental methods for any PDB entry
- Molecular Entities — Retrieve protein chains, nucleic acids, ligands, their sequences, source organisms, and gene names
- Binding Sites & Ligands — Access ligand binding pocket residues, small molecule ligands with formulas and weights
- Quality Assessment — Check resolution, R-factors, and overall quality scores for structure reliability
- UniProt Mappings — Map between UniProt sequence positions and PDB residue numbers
- Biological Assemblies — Understand quaternary structure — monomer, dimer, tetramer, or higher-order complexes
- Structure Search — Full-text Solr search across 200+ PDB metadata fields
- Publications — Find primary citations, PubMed IDs, and related structural studies
The EBI PDBe MCP Server exposes 16 tools through the Vinkius. Connect it to AutoGen in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
All 16 EBI PDBe tools available for AutoGen
When AutoGen connects to EBI PDBe through Vinkius, your AI agent gets direct access to every tool listed below — spanning pdb, protein-structure, 3d-structures, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.
Get assemblies on EBI PDBe
Returns assembly IDs, composition (which entities and how many copies), preferred assembly flag, and form description. Critical for understanding whether a protein functions as a monomer, dimer, tetramer, or higher-order complex. Get biological assembly information (quaternary structure)
Get binding sites on EBI PDBe
Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions
Get cofactors on EBI PDBe
Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations
Get experiment on EBI PDBe
Get experimental method details for a structure
Get ligand monomers on EBI PDBe
Returns chemical component IDs, names, molecular formulas, molecular weights, and their chain/residue positions. Essential for drug discovery and understanding protein-small molecule interactions. Get small molecule ligands bound in the structure
Get modified residues on EBI PDBe
Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides
Get molecules on EBI PDBe
Returns entity IDs, molecule types, names, chain assignments, sequence lengths, molecular weights, source organisms, and gene names. Get molecular entities (chains, polymers) in a structure
Get mutated residues on EBI PDBe
Shows the original residue, mutated residue, chain, and position. Essential for understanding how the crystallized construct differs from the native protein. Get engineered mutations vs. wild-type sequence
Get publications on EBI PDBe
Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs
Get quality scores on EBI PDBe
The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure
Get related entries on EBI PDBe
Useful for discovering alternative conformations, mutants, or complexes of the same protein that have been structurally characterized. Get related PDB entries citing the same publications
Get residue listing on EBI PDBe
Shows residue names, numbers (both PDB and author numbering), organized by entity and chain. Returns a sample of the first 20 residues per chain for efficiency. Get full residue-level inventory per chain
Get secondary structure on EBI PDBe
Shows the count of helices and strands per chain, organized by molecular entity. Essential for understanding protein fold topology. Get helix, sheet, and coil assignments per residue
Get summary on EBI PDBe
Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution
Get uniprot mapping on EBI PDBe
Returns UniProt accessions, chain assignments, and start/end position mappings. Essential for cross-referencing between protein sequence databases and 3D structural data. Get UniProt to PDB residue mappings
Search structures on EBI PDBe
Use natural language queries like "insulin receptor kinase", "SARS-CoV-2 spike protein", "cryo-EM resolution<3", or specific organism names. Returns PDB IDs, titles, methods, resolutions, and organisms. Search PDB structures with full-text queries
Connect EBI PDBe to AutoGen via MCP
Follow these steps to wire EBI PDBe into AutoGen. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install AutoGen
pip install "autogen-ext[mcp]"Replace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenIntegrate into workflow
Explore tools
Why Use AutoGen with the EBI PDBe MCP Server
AutoGen provides unique advantages when paired with EBI PDBe through the Model Context Protocol.
Multi-agent conversations: multiple AutoGen agents discuss, delegate, and collaboratively use EBI PDBe tools to solve complex tasks
Role-based architecture lets you assign EBI PDBe 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 EBI PDBe tool calls
Code execution sandbox: AutoGen agents can write and run code that processes EBI PDBe tool responses in an isolated environment
EBI PDBe + AutoGen Use Cases
Practical scenarios where AutoGen combined with the EBI PDBe MCP Server delivers measurable value.
Collaborative analysis: one agent queries EBI PDBe while another validates results and a third generates the final report
Automated review pipelines: a researcher agent fetches data from EBI PDBe, a critic agent evaluates quality, and a writer produces the output
Interactive planning: agents negotiate task allocation using EBI PDBe data to make informed decisions about resource distribution
Code generation with live data: an AutoGen coder agent writes scripts that process EBI PDBe responses in a sandboxed execution environment
Example Prompts for EBI PDBe in AutoGen
Ready-to-use prompts you can give your AutoGen agent to start working with EBI PDBe immediately.
"Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)."
"What ligands are bound in the hemoglobin structure 4hhb?"
"Search for cryo-EM structures of ribosome complexes."
Troubleshooting EBI PDBe MCP Server with AutoGen
Common issues when connecting EBI PDBe to AutoGen through Vinkius, and how to resolve them.
McpWorkbench not found
pip install "autogen-ext[mcp]"EBI PDBe + AutoGen FAQ
Common questions about integrating EBI PDBe MCP Server with AutoGen.
How does AutoGen connect to MCP servers?
Can different agents have different MCP tool access?
Does AutoGen support human approval for tool calls?
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