EBI Proteins API MCP Server for ClineGive Cline instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more
GDPR Free for SubscribersCline is an autonomous AI coding agent inside VS Code that plans, executes, and iterates on tasks. Wire EBI Proteins API through Vinkius and Cline gains direct access to every tool. from data retrieval to workflow automation. without leaving the terminal.
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The EBI Proteins API MCP Server for Cline is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
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Gemini{
"mcpServers": {
"ebi-proteins-api": {
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
}
}
}Vinkius Desktop App
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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.
Cline operates autonomously inside VS Code. it reads your codebase, plans a strategy, and executes multi-step tasks including EBI Proteins API tool calls without waiting for prompts between steps. Connect 16 tools through Vinkius and Cline can fetch data, generate code, and commit changes in a single autonomous run.
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 Cline 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 Cline
When Cline 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 Cline via MCP
Follow these steps to wire EBI Proteins API into Cline. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Open Cline MCP Settings
Add remote server
Enable the server
Start using EBI Proteins API
Why Use Cline with the EBI Proteins API MCP Server
Cline provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.
Cline operates autonomously. it reads your codebase, plans a strategy, and executes multi-step tasks including MCP tool calls without step-by-step prompts
Runs inside VS Code, so you get MCP tool access alongside your existing extensions, terminal, and version control in a single window
Cline can create, edit, and delete files based on MCP tool responses, enabling end-to-end automation from data retrieval to code generation
Transparent execution: every tool call and file change is shown in Cline's activity log for full visibility and approval before committing
EBI Proteins API + Cline Use Cases
Practical scenarios where Cline combined with the EBI Proteins API MCP Server delivers measurable value.
Autonomous feature building: tell Cline to fetch data from EBI Proteins API and scaffold a complete module with types, handlers, and tests
Codebase refactoring: use EBI Proteins API tools to validate live data while Cline restructures your code to match updated schemas
Automated testing: Cline fetches real responses from EBI Proteins API and generates snapshot tests or mocks based on actual payloads
Incident response: query EBI Proteins API for real-time status and let Cline generate hotfix patches based on the findings
Example Prompts for EBI Proteins API in Cline
Ready-to-use prompts you can give your Cline 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 Cline
Common issues when connecting EBI Proteins API to Cline through Vinkius, and how to resolve them.
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EBI Proteins API + Cline FAQ
Common questions about integrating EBI Proteins API MCP Server with Cline.
How does Cline connect to MCP servers?
Can Cline run MCP tools without approval?
Does Cline support multiple MCP servers at once?
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