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Connect Ebi Proteins API to ChatGPT, Claude and Gemini

Set it up once and it works in ChatGPT, Claude, Cursor, and any other client you love. It all runs safely in the background, so you can relax and focus on what really matters. Pull real-time protein data and genomic mappings into your AI agent.

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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.

ChatGPTClaudeCursorPerplexityGeminiMicrosoft CopilotRaycastMeta AI

Your AI does the work. We keep it safe and sound.

No other AI tool gives you this. Your workflow runs in the client you already love, your account stays protected, and you decide what the agent can and cannot do. It is the whole reason to make the switch.

Each Connector lives inside our infrastructure, the same place where your workflow runs. The three things below are already part of it, working quietly in the background so you never have to think about them. Nothing to add, nothing to set up, nothing to worry about.

A futuristic MCP client docking bay
V8 Isolate01

Each Connector runs inside its own sealed environment.

Each Connector runs inside its own sealed V8 runtime — no access to your files, your system, or other servers. A Connector never sees past its own request.

Kill Switch02

One switch stops every agent. Instantly.

One action deactivates every Connector, revokes every token, and ends every session at once. AI Governance keeps the record.

FinOps per User03

Spending limits that pause instead of surprise.

Every user keeps their own connections and credentials, isolated from everyone else. Anything that would cross your spending limit is held for your approval, not billed.

Three controls, built into the layer your AI connects through.

Curated set · 16 capabilities

We ship only the actions that matter.

Capability set01 / 04

01-04

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 01

    Get antigen

    Retrieves peptide regions from the Human Protein Atlas used for antibody generation. These are experimentally validated targets for immunology research.

  2. 02

    Get genecentric

    Provides a gene-centric view of a proteome using a UniProt Proteome ID. It shows the canonical protein and the count of related proteins for that gene.

  3. 03

    Get protein features

    Fetches sequence feature annotations for a specific protein. This includes domains, binding sites, signal peptides, and disulfide bonds with their position data.

  4. 04

    Get proteome

    Returns details for a specific UniProt Proteome ID. You get taxonomy, protein counts, and reference status for the requested proteome.

Capability set02 / 04

05-08

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 05

    Get proteomics ptm

    Accesses post-translational modification data from mass-spec evidence. It provides residue-level PTM positions and evidence counts.

  2. 06

    Get variation

    Retrieves genetic variants for a protein from multiple sources. It includes wild-type and mutant residues, clinical significance, and consequence types.

  3. 07

    Search features by type

    Searches for specific feature types across different proteins. You can filter by types like DOMAIN, BINDING, ACTIVE_SITE, or SIGNAL.

  4. 08

    Search proteins

    Searches the protein database using gene names, organism names, or keywords. It returns a summary list with names and sequence lengths.

Capability set03 / 04

09-12

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 09

    Search taxonomy

    Finds taxonomy entries by organism name. This helps you identify the correct taxon ID before querying specific proteomes.

  2. 10

    Get coordinates

    Maps a protein to its genome coordinates. It provides Ensembl IDs and chromosome positions for GRCh38 or GRCh37.

  3. 11

    Get mutagenesis

    Retrieves data from mutagenesis experiments. It lists the wild-type and mutant residues along with the functional impact on the phenotype.

  4. 12

    Get protein

    Fetches a full protein entry using a UniProt accession. This is the primary way to get comprehensive protein data.

Capability set04 / 04

13-16

4 capabilities in this set.

Part of 16 available through EMBL-EBI Proteins API.

  1. 13

    Get proteomics

    Provides mass-spectrometry proteomics data for a protein. It shows which peptides were experimentally detected and their uniqueness.

  2. 14

    Get taxonomy

    Returns details for a specific NCBI taxon ID. You get the scientific name, lineage, and parent/child nodes.

  3. 15

    Search proteomes

    Searches for proteomes by organism name. It returns proteome IDs, protein counts, and taxonomy information.

  4. 16

    Search variation

    Searches for genetic variants based on consequence type, source, or residue. This is used to find clinically relevant variants across a proteome.

Real work

What teams actually run

01

Variant Pathogenicity Assessment

A geneticist asks the agent to find all missense mutations in a specific gene to evaluate clinical significance.

02

Protein Domain Mapping

A structural biologist queries the specific binding sites and disulfide bonds of a target protein.

03

Genomic Cross-Referencing

A researcher maps a protein sequence to its exact location on a chromosome for genomic analysis.

04

Proteome Discovery

A bioinformatician searches for all proteins associated with a specific organism or taxon ID.

Automate a task

Put EMBL-EBI Proteins API to work on one thing.

Step-by-step automations your AI runs through this Connector: the workflow, the prompts to start with, and the exact capabilities behind each move.

One connector, every AI

EMBL-EBI Proteins API works with the most popular AI clients.

These are the most popular clients, each with a step-by-step guide: one link, set up once, with governance and visibility built in. And because everything runs on the MCP standard, the same connection also works in any other compatible client — nothing to rebuild.

ClaudeClaudeChatGPTChatGPTGeminiGeminiPerplexityPerplexityGrokGrokMicrosoft CopilotMicrosoft CopilotCursorCursorVS CodeVS CodeWindsurfWindsurfJetBrainsJetBrainsClineClineLangChainLangChainVercel AI SDKVercel AI SDKLovableLovableZ.aiZ.aiRaycastRaycastQwen CodeQwen CodeKimi CodeKimi CodeLe ChatLe Chat

Building your own app? The connector is yours to use.

You don't need a client to put EMBL-EBI Proteins API to work: the same hosted connection plugs into your own applications and agent code, with the same governance on every request. Build with it, chat with it — one connection for both.

Observed, not estimated

997ms average. Fast in production.

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

Daily averagePeak 1413ms
Oct 3Today
Fastest day
903ms
Slowest day
1413ms
14-day trend
Stable+4%

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

Guided setup for Claude? Set up EMBL-EBI Proteins API in Claude and other AIs

See all the AI clients this connector works with ↑

Who it's for

Built for the work EMBL-EBI Proteins API owners hand off.

This MCP is built for researchers working in molecular biology, genetics, and bioinformatics.

  • 01

    Molecular Biologists

    They use the agent to pull protein sequences and functional annotations without manual database searching.

  • 02

    Clinical Geneticists

    They hand off variant interpretation tasks to the agent to pull data from ClinVar and COSMIC.

  • 03

    Bioinformaticians

    They use the agent to programmatically fetch proteome and genome coordinate data for their pipelines.

FAQ

Questions EMBL-EBI Proteins API owners ask.

  • 01

    Do I need an API key for this MCP?

    No. The EBI Proteins API is public, so no credentials or API keys are required to use this connector.

  • 02

    Which AI clients can I use with this?

    You can use this MCP with any compatible client, including Claude, Cursor, and Windsurf.

  • 03

    Where does the protein data come from?

    All data is sourced directly from the official EMBL-EBI Proteins REST API, including UniProtKB data.

  • 04

    Can I get genomic coordinates for proteins?

    Yes. You can use the get_coordinates capability to find Ensembl IDs and chromosome positions for GRCh38 and GRCh37.

  • 05

    Does this include clinical variant data?

    Yes. The MCP accesses curated variants from sources like ClinVar, gnomAD, and COSMIC.

  • 06

    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.

  • 07

    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.

  • 08

    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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