EBI PDBe MCP Server with 16 Tools for Claude, Cursor, and AI Agents
GDPR Free for SubscribersExplore 3D protein structures, ligand interactions, and molecular assemblies from the Protein Data Bank in Europe. Vinkius routes your AI agents directly to EBI PDBe through a governed connection. 16 tools ready to use with Claude, ChatGPT, Cursor, or any AI agent — no hosting, no setup, connect in 30 seconds.
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What is the PDBe (Protein Data Bank in Europe) MCP Server?
The PDBe (Protein Data Bank in Europe) MCP Server routes AI agents like Claude, ChatGPT, and Cursor directly to PDBe (Protein Data Bank in Europe) via 16 tools. Explore 3D protein structures, ligand interactions, and molecular assemblies from the Protein Data Bank in Europe. Powered by Vinkius — your credentials stay on your side of the connection, every request is auditable. Connect in under 2 minutes.
Built-in capabilities (16)
Tools for your AI Agents to operate PDBe (Protein Data Bank in Europe)
Ask your AI agent "Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)." and get the answer without opening a single dashboard. With 16 tools connected to real PDBe (Protein Data Bank in Europe) data, your agents reason over live information, cross-reference it with other MCP servers, and deliver insights you would spend hours assembling manually.
Works with Claude, ChatGPT, Cursor, and any MCP-compatible client. Powered by Vinkius — your credentials never touch the AI model, every request is auditable. Connect in under two minutes.
Why teams choose Vinkius
One subscription gives you the infrastructure to connect your AI agents to thousands of MCP servers — and deploy your own to the Vinkius Edge. Your credentials stay yours. Your data flows directly between your agent and the API. DLP blocks sensitive information from ever reaching the model, kill switch for instant shutdown, and up to 60% token savings. Enterprise-grade routing and governance, zero maintenance.
Build your own MCP Server with our secure development framework →The EBI PDBe App Connector works with every AI agent you already use
…and any MCP-compatible client
Use all 16 EBI PDBe tools with your AI agents right now
Vinkius routes your AI agents to EBI PDBe through a governed proxy. Beyond a simple connection, you get full visibility into every action your agents perform, with enterprise-grade security and up to 60% savings on AI costs.
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
What the EBI PDBe MCP Server unlocks
Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.
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
How it works
1. Subscribe to this server
2. No API key required — the PDBe API is fully public
3. Start querying 3D structures from Claude, Cursor, or any MCP-compatible client
Your AI agent becomes a structural biology research assistant with direct access to every experimentally determined protein structure. All data is sourced from the official PDBe REST API maintained by EMBL-EBI.
Who is this for?
- Structural Biologists — retrieve structure metadata, quality assessments, and experimental parameters without downloading coordinate files
- Drug Discovery Scientists — identify binding sites, ligand interactions, and cofactors for rational drug design
- Bioinformaticians — cross-reference sequence data with 3D structural annotations via UniProt mappings
- Educators & Students — explore real macromolecular structures for teaching protein chemistry and structural biology
Frequently asked questions about the EBI PDBe MCP Server
Do I need an API key?
No. The PDBe API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.
What types of structures are available?
The PDBe contains over 200,000 experimentally determined 3D structures of proteins, nucleic acids, and complex assemblies. Structures are determined by X-ray crystallography, cryo-electron microscopy (cryo-EM), NMR spectroscopy, and other methods. This includes enzymes, receptors, antibodies, viral proteins, ribosomes, and drug-target complexes.
Can I find drug binding sites?
Yes. Use get_binding_sites to retrieve all annotated ligand binding pockets with their constituent residues. Combine with get_ligand_monomers to identify the small molecules bound in the structure, and get_cofactors for prosthetic groups. This workflow is essential for structure-based drug design and virtual screening target preparation.
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We built the connector to EBI PDBe. Now put your agents to work. Fully governed.
Vinkius is the AI Gateway with managed hosting. Stop building connectors. Every connection runs inside eight layers of security.
Hosted, sandboxed, and live on AWS. You don't provision anything. You don't maintain anything. You connect.
Every tool call, every token, every response. Logged and auditable. Data flows direct from EBI PDBe to your agent. Nothing is stored on our side. Ever.
Eight governance layers on every request. Sensitive data redacted before it reaches the model. Kill switch if anything goes sideways. Always on.