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Use PDBe (Protein Data Bank in Europe) with your AI.

Connect your account once and let the AI you already use work with it, without building another integration. Explore 3D protein structures, ligand interactions, and molecular assemblies from the Protein Data Bank in Europe.

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Works with modern AI clients that support MCP, including ChatGPT, Claude, Cursor, and more.

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Complete set · 16 capabilities

The complete PDBe (Protein Data Bank in Europe) capability set.

These are the exact actions your AI can choose when you ask it to work with PDBe (Protein Data Bank in Europe).

Capability set01 / 04

01-04

4 capabilities in this set.

Part of 16 available through PDBe (Protein Data Bank in Europe).

  1. 01

    Get cofactors

    Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations

  2. 02

    Get experiment

    Get experimental method details for a structure

  3. 03

    Get modified residues

    Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides

  4. 04

    Get molecules

    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

Capability set02 / 04

05-08

4 capabilities in this set.

Part of 16 available through PDBe (Protein Data Bank in Europe).

  1. 05

    Get mutated residues

    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

  2. 06

    Get quality scores

    The first thing a structural biologist checks when evaluating a structure for reliability. Get globalThis quality metrics for a structure

  3. 07

    Get related entries

    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

  4. 08

    Get residue listing

    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

Capability set03 / 04

09-12

4 capabilities in this set.

Part of 16 available through PDBe (Protein Data Bank in Europe).

  1. 09

    Get summary

    Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution

  2. 10

    Get uniprot mapping

    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

  3. 11

    Get assemblies

    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)

  4. 12

    Get binding sites

    Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions

Capability set04 / 04

13-16

4 capabilities in this set.

Part of 16 available through PDBe (Protein Data Bank in Europe).

  1. 13

    Get ligand monomers

    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

  2. 14

    Get publications

    Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs

  3. 15

    Get secondary structure

    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

  4. 16

    Search structures

    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

Observed, not estimated

902ms average. Fast in production.

PDBe (Protein Data Bank in Europe) is checked daily against the live service.

Daily averagePeak 1078ms
Aug 20Today
Fastest day
813ms
Slowest day
1078ms
14-day trend
Slowing+13%

Connect your client

One URL. Every client.

Activate the Connector, copy your link, and paste it into the client you already use. 16 capabilities arrive ready to run.

Preview access · not provider authentication

The vk_preview_* token belongs to Vinkius preview infrastructure. It lets Claude discover and display the capabilities of PDBe (Protein Data Bank in Europe), so you can see the experience inside your AI.

It does not authenticate your account with PDBe (Protein Data Bank in Europe). Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

PDBe (Protein Data Bank in Europe) Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_bI09khwqGh15yaAARSveb5XxpbscMGTIKjQ4vrCZ/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — PDBe (Protein Data Bank in Europe) capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ebi-pdbe-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_bI09khwqGh15yaAARSveb5XxpbscMGTIKjQ4vrCZ/mcp"
    }
  }
}
  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Step-by-step instructions for each client are in the guide. How to connect

FAQ

Questions PDBe (Protein Data Bank in Europe) owners ask.

  • 01

    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.

  • 02

    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.

  • 03

    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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