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Use EMBL-EBI Proteins API with your AI.

Connect your account once and let the AI you already use work with it, without building another integration. Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries.

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Developed, maintained, and hosted by Vinkius.

MCP VERIFIED · PRODUCTION READY · VINKIUS GUARANTEED

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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 EMBL-EBI Proteins API capability set.

These are the exact actions your AI can choose when you ask it to work with EMBL-EBI Proteins API.

Capability set01 / 04

01-04

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 01

    Get antigen

    These are peptide regions used for antibody generation, indicating experimentally validated protein expression targets. Useful for immunology and antibody-based research. Get antigen sequences from Human Protein Atlas

  2. 02

    Get genecentric

    Shows canonical protein and related protein count for each gene. Use with a UniProt Proteome ID (e.g. UP000005640). Get the gene-centric view of a proteome

  3. 03

    Get protein features

    Features include domains, binding sites, active sites, signal peptides, transmembrane regions, disulfide bonds, glycosylation sites, and more. Each feature has start/end positions and evidence counts. Get sequence feature annotations for a protein

  4. 04

    Get proteome

    Returns taxonomy, protein count, gene count, reference status, and component information. Use IDs like UP000005640 for human proteome or UP000000589 for mouse. Get a specific proteome by UniProt Proteome ID

Capability set02 / 04

05-08

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 05

    Get proteomics ptm

    Provides residue-level PTM positions with evidence counts. Get post-translational modifications from mass-spec data

  2. 06

    Get variation

    Each variant includes wild-type and mutant residues, clinical significance, consequence type (e.g. missense, nonsense), and cross-references. Critical for clinical genomics and variant interpretation. Get genetic variants for a protein from multiple sources

  3. 07

    Search features by type

    Valid types include: DOMAIN, BINDING, ACTIVE_SITE, SIGNAL, TRANSMEM, DISULFID, CARBOHYD, MOD_RES, VARIANT, MUTAGEN, REGION, MOTIF, SITE, REPEAT, COILED, COMPBIAS, HELIX, STRAND, TURN. Search features by type across proteins

  4. 08

    Search proteins

    You can combine gene name (e.g. TP53), organism (e.g. human, 9606), keyword (e.g. kinase), or accession. Returns a summarized list of matching proteins with names, organisms, and sequence lengths. Search proteins by gene name, organism, or keyword

Capability set03 / 04

09-12

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 09

    Search taxonomy

    Returns matching taxonomy entries with scientific names, common names, taxon IDs, and ranks. Useful for finding the correct taxon ID before querying proteins or proteomes for a specific organism. Search taxonomy by organism name

  2. 10

    Get coordinates

    Returns Ensembl gene, transcript, and translation IDs along with chromosome, start/end positions, and strand information. Essential for bridging protein annotations with genomic data. Get genome coordinate mappings for a protein

  3. 11

    Get mutagenesis

    Each entry includes the wild-type and mutant residues, position, and a description of the functional impact. Critical for understanding structure-function relationships. Get mutagenesis experiments and phenotypic effects

  4. 12

    Get protein

    Use a UniProt accession such as P12345, Q9Y6K9, or P53_HUMAN. Retrieve a full protein entry by UniProt accession

Capability set04 / 04

13-16

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 13

    Get proteomics

    Shows which peptides have been experimentally detected and whether they are unique to this protein. Essential for validating protein expression. Get mass-spectrometry proteomics data for a protein

  2. 14

    Get taxonomy

    Returns scientific name, common name, rank, lineage, parent, and children nodes. Use IDs like 9606 for human, 10090 for mouse, 562 for E. coli. Get taxonomy node details by NCBI taxon ID

  3. 15

    Search proteomes

    Returns proteome IDs, taxonomy, protein counts, gene counts, and reference proteome status. Use queries like "homo sapiens", "escherichia coli", "arabidopsis". Search proteomes by organism name

  4. 16

    Search variation

    G. large_scale_study, uniprot, mixed), consequence type (e.g. missense, stop gained), and wild-type residue. Use this to find clinically relevant variants across the proteome. Search variants by consequence type, source, or residue

Observed, not estimated

936ms average. Fast in production.

EMBL-EBI Proteins API is checked daily against the live service.

Daily averagePeak 1250ms
Aug 20Today
Fastest day
789ms
Slowest day
1250ms
14-day trend
Slowing+21%

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 EMBL-EBI Proteins API, so you can see the experience inside your AI.

It does not authenticate your account with EMBL-EBI Proteins API. Actions requiring credentials or live account data may not run until you activate the Connector and authorize the service.

EMBL-EBI Proteins API Connector

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

Connector linkhttps://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/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 — EMBL-EBI Proteins API capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/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 EMBL-EBI Proteins API owners ask.

  • 01

    Do I need an API key to use this server?

    No. The EMBL-EBI Proteins API is completely public and requires no authentication. Simply subscribe to this server and enter any placeholder value in the API key field to start querying protein data immediately.

  • 02

    What kind of variant data is available?

    The server aggregates genetic variants from multiple authoritative sources: UniProtKB curated variants, ClinVar clinical significance data, gnomAD population frequencies, 1000 Genomes Project, COSMIC somatic mutations, TOPMed whole-genome sequencing, ExAC exome data, and TCGA cancer variants. Each variant includes consequence type, clinical significance, and source cross-references.

  • 03

    Can I map protein positions to genome coordinates?

    Yes. The get_coordinates capability maps any UniProt protein to reference genome coordinates on GRCh38 and GRCh37 assemblies. It returns Ensembl gene, transcript, and translation identifiers along with chromosome, start/end positions, and strand orientation. This bridges the gap between protein-level annotations and genomic-level analyses.

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