EBI Proteins API MCP, Ready to Go
Use the EBI Proteins API MCP with Claude or Cursor to pull protein sequences, genetic variants, and proteomics data from the UniProt database.
No credit card required. Experience the power of this integration risk-free.
Query the UniProt knowledge base for protein sequences and genetic variants.
Works with every AI agent you already use
…and any MCP-compatible client
How fast is the EBI Proteins API MCP Server?
Average time for the server to become ready for requests over the last 14 days, measured until the initialize / tools/list handshake completes. Metrics are updated daily between 00:00 and 04:00 UTC. Create a free account, use this MCP on Vinkius Cloud, and connect it to your AI agent in seconds.
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What AI agents can do with EBI Proteins API 16 Tools for Bioinformatics
Access protein sequences, genetic variants, and proteomics data through 16 specific tools.
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.
Get mutagenesis
Retrieve mutagenesis experiments and their phenotypic effects. This helps you understand how specific mutations impact protein structure and function.
Get protein
Fetch a complete protein entry using a UniProt accession. Use this to get names, sequences, and cross-references in one go.
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.
Get proteomics
Access mass-spectrometry proteomics data for a protein. This lets you see which peptides were experimentally detected and if they're unique.
Get proteomics ptm
Retrieve residue-level post-translational modification positions. Use this to see evidence counts from mass-spec data.
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.
Get variation
Fetch genetic variants from sources like ClinVar and gnomAD. This provides clinical significance and consequence types for protein mutations.
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.
Search proteins
Search for proteins using gene names, organisms, or keywords. This returns a summary list of matching proteins and their sequence lengths.
Search proteomes
Search for proteomes by organism name like "homo sapiens". This helps you find the correct proteome ID for a specific species.
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.
Search variation
Search for clinically relevant variants by consequence type or source. Use this to find specific types of mutations across the proteome.
Get antigen
Retrieve peptide regions used for antibody generation. This is useful for identifying validated expression targets in immunology research.
Get coordinates
Map a protein to genome coordinates on GRCh38 or GRCh37. This bridges protein annotations with Ensembl gene and transcript IDs.
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.
One MCP enables access. Vinkius turns MCPs into production-ready infrastructure.
You're looking at one of 5,700+ managed MCPs. The real value isn't the catalog. It's the control plane that secures, governs, audits, and manages every interaction between your agents and the tools they use.
No Shadow AI
Every agent action is visible, approved, and auditable. Nothing runs outside your governance.
Absolute agent control
Fine-grained permissions for every agent, MCP, and tool. Instantly revoke access and audit every execution.
Cost control per token
Spend broken down to the token, tool, and agent. Budgets and hard limits. No surprise invoices.
Managed & monitored infra
We operate the runtime, authentication, scaling, retries, and monitoring. Your team manages AI, not infrastructure.
Data protection, DLP by design
Sensitive data is filtered before reaching the model. Access is governed so agents receive only the information they're allowed to use.
Token optimization, real savings
Lower AI costs by delivering the right context instead of unnecessary tools. Better accuracy, faster responses, and fewer wasted tokens.
EBI Proteins API for Faster Bioinformatics Data Retrieval
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.
Frequently Asked Questions
Can I use the EBI Proteins API MCP to get protein sequences? +
Yes, you can use this MCP 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 MCP 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 MCP 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 tools within the MCP 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 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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