• MAPPING
  • ANALYSIS
  • VALIDATION
  • HUMAN

How to map UniProt sequences to PDB residues with your AI

Connect EBI PDBe to your AI client to bridge the gap between protein sequences and 3D structures. Once connected, your agent handles the coordinate translations for you.

Ask AI about this page

Short answer

How do I map UniProt positions to PDB residues?

Your AI uses the get_uniprot_mapping tool to translate UniProt accession positions into specific 3D structural residue numbers. This allows you to pinpoint exactly where a sequence segment sits in a 3D model. You get a direct mapping of sequence coordinates to structural coordinates.

Mapping outcomes

Where your data lands

The AI turns sequence data into structural context.

MAPPING

Coordinate translation

The AI finds the exact residue numbers in a PDB file that correspond to your UniProt sequence. You get the precise structural location of any given sequence range.

ANALYSIS

Spatial context

Once the mapping is done, your agent can identify which structural features, like active sites or binding pockets, align with your specific UniProt residues.

VALIDATION

Structural verification

You can check if specific mutations or sequence changes in UniProt will land on critical residues within the 3D structure.

HUMAN

Manual review

You must review the final residue mappings to ensure they align with your specific structural model or experimental data before running downstream simulations.

The workflow

What your AI does when the sequence arrives.

The AI handles the heavy lifting of cross-referencing databases.

  1. Identify sequence range

    Your agent parses your request to identify the specific UniProt accession and the residue range you want to locate.

    get_uniprot_mapping

  2. Execute mapping

    The AI calls the mapping tool to pull the relationship between the UniProt sequence and the PDB structure.

    get_uniprot_mapping

  3. Translate coordinates

    The agent converts the sequence-based positions into the specific residue numbering used in the 3D structural file.

    get_uniprot_mapping

  4. Format results

    The AI presents the mapping in a clear list or table so you can immediately use the residue numbers for your analysis.

    get_uniprot_mapping

Try it

Copy these to start.

Use these prompts to trigger the mapping process.

Starting points

Swap out the UniProt IDs and residue ranges with your actual research data.

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"
    }
  }
}
Copy into chat04

  • Map UniProt accession P12345 residues 50 to 100 to their corresponding PDB residue numbers.

  • Find the PDB residue mapping for the following UniProt sequence range: [insert range].

  • Which PDB residues correspond to the active site residues in UniProt P67890?

  • Give me a list of all PDB residue numbers that map to the sequence segment in UniProt Q12345.

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Start here

Connect EBI PDBe once, then ask.

Connect the EBI PDBe MCP to your preferred client with one click. Your credentials stay encrypted, and you can start mapping immediately.

Connect EBI PDBe to your AI

FAQ

How this task behaves

  • 01

    Can the AI automatically download the PDB files?

    No. The AI uses the mapping tool to find residue numbers, but it does not download or manipulate the raw structural files themselves.

  • 02

    Does the AI update the UniProt database?

    No. The AI only reads data from EBI PDBe to perform the mapping. It cannot change or write to UniProt or PDB databases.

  • 03

    Can I map multiple UniProt accessions at once?

    Yes, you can ask your agent to process a list of accessions or multiple residue ranges in a single prompt.

  • 04

    What happens if a sequence has no structural mapping?

    If the tool cannot find a corresponding structural entry in PDBe for that UniProt sequence, the AI will tell you that no mapping exists.

  • 05

    Does the AI handle protein complex mappings?

    Yes, as long as the mapping is available in the PDBe database, the AI can retrieve the residue numbers for the relevant structures.

  • More questions about EBI PDBe? The Connector page answers them. See everything the EBI PDBe Connector can do

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