EBI Proteins API MCP Server for Claude DesktopGive Claude Desktop instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more
GDPR Free for SubscribersClaude Desktop is Anthropic's native application for interacting with Claude AI models on macOS and Windows. It was the first consumer application to ship with built-in MCP support, making it the reference implementation for the Model Context Protocol standard.
Ask AI about this MCP Server for Claude Desktop
The EBI Proteins API MCP Server for Claude Desktop is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Gemini{
"mcpServers": {
"ebi-proteins-api": {
// Your Vinkius token. get it at cloud.vinkius.com
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}Vinkius Desktop App
The modern way to manage MCP Servers — no config files, no terminal commands. Install EBI Proteins API and 4,000+ MCP Servers from a single visual interface.
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About EBI Proteins API MCP Server
Connect to the EMBL-EBI Proteins API and access comprehensive protein biology data from one of the world's leading bioinformatics institutes.
Claude Desktop is the definitive way to connect EBI Proteins API to your AI workflow. Add Vinkius Edge URL to your config, restart the app, and Claude immediately exposes all 16 tools in the chat interface. ask a question, Claude calls the right tool, and you see the answer. Zero code, zero context switching.
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
The EBI Proteins API MCP Server exposes 16 tools through the Vinkius. Connect it to Claude Desktop in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
All 16 EBI Proteins API tools available for Claude Desktop
When Claude Desktop connects to EBI Proteins API through Vinkius, your AI agent gets direct access to every tool listed below — spanning proteins, uniprot, bioinformatics, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.
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
Connect EBI Proteins API to Claude Desktop via MCP
Follow these steps to wire EBI Proteins API into Claude Desktop. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Open Claude Desktop Settings
claude_desktop_config.jsonAdd the MCP Server
mcpServers sectionRestart Claude Desktop
Start using EBI Proteins API
Why Use Claude Desktop with the EBI Proteins API MCP Server
Claude Desktop by Anthropic provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.
Claude Desktop is the reference MCP client. it was designed alongside the protocol itself, ensuring the most complete and stable MCP implementation available
Zero-code configuration: add a server URL to a JSON file and Claude instantly discovers and exposes all available tools in the chat interface
Claude's extended thinking capability lets it reason through multi-step tool usage, chaining multiple API calls to answer complex questions
Enterprise-grade security with local config storage. your tokens never leave your machine, and connections go directly to Vinkius Edge network
EBI Proteins API + Claude Desktop Use Cases
Practical scenarios where Claude Desktop combined with the EBI Proteins API MCP Server delivers measurable value.
Interactive data exploration: ask Claude to query DNS records, look up WHOIS data, and cross-reference results in a single conversation
Ad-hoc security audits: type a domain name and let Claude enumerate subdomains, check DNS history, and flag configuration anomalies. all through natural language
Executive briefings: generate comprehensive domain intelligence reports by asking Claude to compile findings into a formatted summary
Learning and training: new team members can explore API capabilities conversationally without needing to read documentation
Example Prompts for EBI Proteins API in Claude Desktop
Ready-to-use prompts you can give your Claude Desktop agent to start working with EBI Proteins API immediately.
"Get all known genetic variants for the TP53 tumor suppressor protein."
"Show me the domain architecture and binding sites of the EGFR protein."
"Map the BRCA1 protein to its genome coordinates on GRCh38."
Troubleshooting EBI Proteins API MCP Server with Claude Desktop
Common issues when connecting EBI Proteins API to Claude Desktop through Vinkius, and how to resolve them.
Server not appearing after restart
~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\\Claude\\ (Windows).Authentication error
Tools not showing in chat
EBI Proteins API + Claude Desktop FAQ
Common questions about integrating EBI Proteins API MCP Server with Claude Desktop.
How does Claude Desktop discover MCP tools?
claude_desktop_config.json file and connects to each configured MCP server. It calls the tools/list endpoint to fetch the schema for every available tool, then surfaces them as clickable options in the chat interface via the 🔌 icon.What happens if the MCP server is temporarily unavailable?
Can I connect multiple MCP servers simultaneously?
mcpServers section of the config file. Each server appears as a separate tool provider, and Claude can use tools from multiple servers in a single conversation turn.Is there a limit on the number of tools per server?
Does Claude Desktop support Streamable HTTP transport?
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