EMBL-EBI Proteins API Connector for AI agents.
16 live capabilities
Query the UniProt knowledge base for protein sequences and genetic variants.
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Why people use EMBL-EBI Proteins API
EBI Proteins API for Faster Bioinformatics Data Retrieval
This Connector changes that by putting the EMBL-EBI Proteins API directly into your AI client. You can ask your agent to pull everything from sequence features and binding sites to complex proteomics data in a single request. You get the data you need in seconds, ready for your next step.
What Vinkius changes
You get instant, programmatic access to the world's largest protein database without needing an API key.
Use it from Claude, ChatGPT, Cursor or another AI client you already have.
One account · 5,900+ Connectors
- Real-world use case 01
Variant Analysis
A clinical geneticist asks for all known mutations of a specific tumor suppressor protein.
- Real-world use case 02
Structural Mapping
A structural biologist needs to find all binding sites for a specific enzyme.
- Real-world use case 03
Genomic Alignment
A bioinformatician needs to map a protein to its specific chromosome position.
Complete set · 16capabilities
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.
01—04
4 capabilities in this set.
Part of 16 available through EMBL-EBI Proteins API.
- 01 Capability
Get proteomics
Access mass-spectrometry proteomics data for a protein. This lets you see which peptides were experimentally detected and if they're unique.
- 02 Capability
Get antigen
Retrieve peptide regions used for antibody generation. This is useful for identifying validated expression targets in immunology research.
- 03 Capability
Get coordinates
Map a protein to genome coordinates on GRCh38 or GRCh37. This bridges protein annotations with Ensembl gene and transcript IDs.
- 04 Capability
Get protein features
Get sequence annotations including domains, active sites, and disulfide bonds. Use this to see the physical features of a protein's structure.
05—08
4 capabilities in this set.
Part of 16 available through EMBL-EBI Proteins API.
- 05 Capability
Get genecentric
Get the gene-centric view of a proteome including canonical protein counts. Use this to see how many proteins relate to each gene in a specific proteome.
- 06 Capability
Get mutagenesis
Retrieve mutagenesis experiments and their phenotypic effects. This helps you understand how specific mutations impact protein structure and function.
- 07 Capability
Get protein
Fetch a complete protein entry using a UniProt accession. Use this to get names, sequences, and cross-references in one go.
- 08 Capability
Get proteome
Get details for a specific proteome, including taxonomy and protein counts. Use this to identify the components of a specific organism's proteome.
09—12
4 capabilities in this set.
Part of 16 available through EMBL-EBI Proteins API.
- 09 Capability
Get proteomics ptm
Retrieve residue-level post-translational modification positions. Use this to see evidence counts from mass-spec data.
- 10 Capability
Get taxonomy
Get scientific names, ranks, and lineage for a specific NCBI taxon ID. Use this to navigate the tree of life for a specific organism.
- 11 Capability
Get variation
Fetch genetic variants from sources like ClinVar and gnomAD. This provides clinical significance and consequence types for protein mutations.
- 12 Capability
Search features by type
Search for specific features like domains, binding sites, or signal peptides across proteins. Use this to find specific structural motifs quickly.
13—16
4 capabilities in this set.
Part of 16 available through EMBL-EBI Proteins API.
- 13 Capability
Search proteins
Search for proteins using gene names, organisms, or keywords. This returns a summary list of matching proteins and their sequence lengths.
- 14 Capability
Search proteomes
Search for proteomes by organism name like "homo sapiens". This helps you find the correct proteome ID for a specific species.
- 15 Capability
Search taxonomy
Find taxonomy entries by organism name to get the correct taxon ID. Use this as a first step before querying specific proteins or proteomes.
- 16 Capability
Search variation
Search for clinically relevant variants by consequence type or source. Use this to find specific types of mutations across the proteome.
Set up in minutes
One URL. Then ask EMBL-EBI Proteins API to work.
Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use EMBL-EBI Proteins API from the conversation.
Choose your client
Live previewAdvanced clients IDE · CLI
Claude · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp - Step 01
Open Connectors
In Claude Web or Claude Desktop, open Settings and choose Connectors.
- Step 02
Add the URL
Choose Add custom connector, name it EMBL-EBI Proteins API, and paste the URL above.
- Step 03
Turn it on in chat
Select +, open Connectors, and enable EMBL-EBI Proteins API for the conversation.
ChatGPT · Web + desktop
Connector URL · ready to paste
Streamable HTTPhttps://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp - Step 01
Open MCP settings
On desktop, open Settings and MCP servers. On web, open your workspace app or connector settings.
- Step 02
Add the URL
Choose Add server with Streamable HTTP, or create a custom MCP app, then paste the EMBL-EBI Proteins API URL.
- Step 03
Save and start
Save the connection and enable EMBL-EBI Proteins API in your conversation. Desktop may ask you to restart once.
Cursor · IDE configuration
Advanced setup
{
"mcpServers": {
"ebi-proteins-api": {
"url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
}
}
}- Step 01
Open MCP Settings
Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"
- Step 02
Add the server config
Paste the JSON configuration above into the mcp.json file that opens
- Step 03
Save the file
Cursor will automatically detect the new Connector
- Step 04
Start using EMBL-EBI Proteins API
Open Agent mode in chat and ask: "Using EMBL-EBI Proteins API, help me...". 16 tools available
VS Code Copilot · IDE configuration
Advanced setup
{
"mcpServers": {
"ebi-proteins-api": {
"url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
}
}
}- Step 01
Create MCP config
Create a .vscode/mcp.json file in your project root
- Step 02
Add the server config
Paste the JSON configuration above
- Step 03
Enable Agent mode
Open GitHub Copilot Chat and switch to Agent mode using the dropdown
- Step 04
Start using EMBL-EBI Proteins API
Ask Copilot: "Using EMBL-EBI Proteins API, help me...". 16 tools available
Windsurf · IDE configuration
Advanced setup
{
"mcpServers": {
"ebi-proteins-api": {
"url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
}
}
}- Step 01
Open MCP Settings
Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"
- Step 02
Add the server
Paste the JSON configuration above into mcp_config.json
- Step 03
Save and reload
Windsurf will detect the new server automatically
- Step 04
Start using EMBL-EBI Proteins API
Open Cascade and ask: "Using EMBL-EBI Proteins API, help me...". 16 tools available
Cline · IDE configuration
Advanced setup
{
"mcpServers": {
"ebi-proteins-api": {
"url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
}
}
}- Step 01
Open Cline MCP Settings
Click the Connectors icon in the Cline sidebar panel
- Step 02
Add remote server
Click "Add Connector" and paste the configuration above
- Step 03
Enable the server
Toggle the server switch to ON
- Step 04
Start using EMBL-EBI Proteins API
Ask Cline: "Using EMBL-EBI Proteins API, help me...". 16 tools available
Claude Code · Terminal command
Advanced setup
claude mcp add ebi-proteins-api --transport http "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"- Step 01
Install Claude Code
Run npm install -g @anthropic-ai/claude-code if not already installed
- Step 02
Add the Connector
Run the command above in your terminal
- Step 03
Verify the connection
Run claude mcp to list connected servers, or type /mcp inside a session
- Step 04
Start using EMBL-EBI Proteins API
Ask Claude: "Using EMBL-EBI Proteins API, show me...". 16 tools are ready
Where the request belongs
Work EMBL-EBI Proteins API can move forward.
This is for the researchers who are tired of manual data entry and want to automate the bridge between protein sequences and genomic data.
Molecular Biologist
Pulling sequences and domain architectures to guide experimental design on a Tuesday afternoon.
Clinical Geneticist
Assessing variant pathogenicity using aggregated clinical data for patient reports.
Structural Biologist
Finding binding sites and mutagenesis results to model protein interactions.
Bioinformatician
Mapping proteomes and taxonomy for automated pipeline integration.
Build the capability set
Add more capabilities.
Each Connector adds new actions and data without changing how you work.
Browse ConnectorsUniProt
Search 250M+ protein sequences with functional annotations, gene names, subcellular locations, and amino acid data from the world's most comprehensive protein knowledge base.
EBI InterPro
Classify protein sequences into families, predict functional domains, and explore evolutionary relationships across species.
Ensembl
Access genomic data, gene trees, homologies, and cross-references from the Ensembl database directly from any AI agent.
EBI PDBe
Explore 3D protein structures, ligand interactions, and molecular assemblies from the Protein Data Bank in Europe.
GenBank/NCBI API
Access genomic data. audit sequences, proteins, and UIDs via IA.
KEGG
Access the Kyoto Encyclopedia of Genes and Genomes (KEGG) to query genomic, chemical, and systemic functional information directly from your AI agent.
Bring your own AI
Change the model, client or framework. Keep EMBL-EBI Proteins API connected.
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Claude -
ChatGPT -
Gemini -
Cursor -
VS Code -
Windsurf -
ZCode -
Cline -
Zed -
Continue -
Kiro -
Roo Code -
Zencoder -
Goose -
Void -
Augment Code -
Amp -
Qodo -
Tabnine -
Pieces -
Sourcegraph Cody -
JetBrains -
Warp -
Amazon Q -
Antigravity -
BoltAI -
Raycast -
Jan -
LM Studio -
AnythingLLM -
Open WebUI -
Msty -
Cherry Studio -
LibreChat -
TypingMind -
Chorus -
5ire -
n8n -
LangChain -
LlamaIndex -
CrewAI -
Vercel AI SDK
Before you connect
Questions about EMBL-EBI Proteins API.
The practical details behind the request, access and result.
Can I use the EBI Proteins API MCP to get protein sequences?
Yes, you can use this Connector to pull full protein sequences, names, and cross-references for any UniProt accession. It's a fast way to get the raw data you need for your research.
Does the EBI Proteins API MCP require an API key?
No, the EBI Proteins API is fully public, so you don't need to worry about managing keys or subscriptions. You can start querying data as soon as you connect it.
Can I find clinical variants like those from ClinVar using this?
Yes, this Connector pulls aggregated genetic variant data from sources like ClinVar and gnomAD. It's great for seeing clinical significance and consequence types for mutations.
Does this Connector support genome mapping?
Yes, it can map proteins to specific coordinates on the GRCh38 and GRCh37 assemblies. It provides Ensembl gene and transcript IDs to help link proteins to genomic data.
Can I use the EBI Proteins API MCP for proteomics research?
Absolutely. You can query mass-spectrometry proteomics data, including peptide evidence and post-translational modifications (PTMs).
How do I find the correct taxonomy ID for a specific organism?
You can use the search capabilities within the Connector to find the correct NCBI taxon ID by organism name. This ensures you're querying the right data for your species.
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.
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.
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.
One connection away
Give your agent a direct line to EMBL-EBI Proteins API.
Connect EMBL-EBI Proteins API once. Keep it beside 5,900+ managed Connectors when the next task needs more.
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