EBI Proteins API MCP Server with 16 Tools for Claude, Cursor, and AI Agents
GDPR Free for SubscribersQuery the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries. Vinkius routes your AI agents directly to EBI Proteins API through a governed connection. 16 tools ready to use with Claude, ChatGPT, Cursor, or any AI agent — no hosting, no setup, connect in 30 seconds.
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What is the EMBL-EBI Proteins API MCP Server?
The EMBL-EBI Proteins API MCP Server routes AI agents like Claude, ChatGPT, and Cursor directly to EMBL-EBI Proteins API via 16 tools. Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries. Powered by Vinkius — your credentials stay on your side of the connection, every request is auditable. Connect in under 2 minutes.
Built-in capabilities (16)
Tools for your AI Agents to operate EMBL-EBI Proteins API
Ask your AI agent "Get all known genetic variants for the TP53 tumor suppressor protein." and get the answer without opening a single dashboard. With 16 tools connected to real EMBL-EBI Proteins API data, your agents reason over live information, cross-reference it with other MCP servers, and deliver insights you would spend hours assembling manually.
Works with Claude, ChatGPT, Cursor, and any MCP-compatible client. Powered by Vinkius — your credentials never touch the AI model, every request is auditable. Connect in under two minutes.
Why teams choose Vinkius
One subscription gives you the infrastructure to connect your AI agents to thousands of MCP servers — and deploy your own to the Vinkius Edge. Your credentials stay yours. Your data flows directly between your agent and the API. DLP blocks sensitive information from ever reaching the model, kill switch for instant shutdown, and up to 60% token savings. Enterprise-grade routing and governance, zero maintenance.
Build your own MCP Server with our secure development framework →The EBI Proteins API App Connector works with every AI agent you already use
…and any MCP-compatible client
Use all 16 EBI Proteins API tools with your AI agents right now
Vinkius routes your AI agents to EBI Proteins API through a governed proxy. Beyond a simple connection, you get full visibility into every action your agents perform, with enterprise-grade security and up to 60% savings on AI costs.
Get antigen on EBI Proteins API
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
Get coordinates on EBI Proteins API
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
Get genecentric on EBI Proteins API
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
Get mutagenesis on EBI Proteins API
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
Get protein on EBI Proteins API
Use a UniProt accession such as P12345, Q9Y6K9, or P53_HUMAN. Retrieve a full protein entry by UniProt accession
Get protein features on EBI Proteins API
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
Get proteome on EBI Proteins API
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
Get proteomics on EBI Proteins API
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
Get proteomics ptm on EBI Proteins API
Provides residue-level PTM positions with evidence counts. Get post-translational modifications from mass-spec data
Get taxonomy on EBI Proteins API
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
Get variation on EBI Proteins API
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
Search features by type on EBI Proteins API
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
Search proteins on EBI Proteins API
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
Search proteomes on EBI Proteins API
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
Search taxonomy on EBI Proteins API
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
Search variation on EBI Proteins API
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
What the EBI Proteins API MCP Server unlocks
Connect to the EMBL-EBI Proteins API and access comprehensive protein biology data from one of the world's leading bioinformatics institutes.
What you can do
- Protein Retrieval — Fetch complete protein entries by UniProt accession with names, organisms, gene information, sequences, and cross-references
- Sequence Features — Retrieve annotated domains, binding sites, active sites, signal peptides, transmembrane regions, and disulfide bonds for any protein
- Genetic Variants — Access curated variants from UniProtKB aggregated with large-scale studies including ClinVar, gnomAD, 1000 Genomes, COSMIC, and TOPMed
- Proteomics & PTMs — Query mass-spectrometry peptide evidence and post-translational modifications from PeptideAtlas, MaxQB, EPD, and ProteomicsDB
- Mutagenesis — Explore curated mutagenesis experiments with detailed phenotypic effect descriptions
- Proteomes & Taxonomy — Search reference proteomes and navigate the taxonomy tree by ID or organism name
- Genome Coordinates — Map proteins to genome positions on GRCh38/GRCh37 with Ensembl gene, transcript, and translation IDs
How it works
1. Subscribe to this server
2. No API key required — the EBI Proteins API is fully public
3. Start querying protein data from Claude, Cursor, or any MCP-compatible client
Your AI agent becomes a molecular biology research assistant with direct access to the entire UniProt protein knowledge base. All data is sourced from the official EMBL-EBI Proteins REST API.
Who is this for?
- Molecular Biologists — retrieve protein sequences, domain architectures, and functional annotations without navigating complex web databases
- Clinical Geneticists — access aggregated variant data from ClinVar, gnomAD, and COSMIC for variant interpretation and pathogenicity assessment
- Structural Biologists — query sequence features, binding sites, and mutagenesis data to guide experimental design
- Bioinformaticians — programmatically access proteomes, taxonomy, and genome coordinate mappings for pipeline integration
Frequently asked questions about the EBI Proteins API MCP Server
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 tool 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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We built the connector to EBI Proteins API. Now put your agents to work. Fully governed.
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Every tool call, every token, every response. Logged and auditable. Data flows direct from EBI Proteins API to your agent. Nothing is stored on our side. Ever.
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