EBI Proteins API MCP Server for CrewAIGive CrewAI instant access to 16 tools to Get Antigen, Get Coordinates, Get Genecentric, and more
GDPR Free for SubscribersConnect your CrewAI agents to EBI Proteins API through Vinkius, pass the Edge URL in the `mcps` parameter and every EBI Proteins API tool is auto-discovered at runtime. No credentials to manage, no infrastructure to maintain.
Ask AI about this MCP Server for CrewAI
The EBI Proteins API MCP Server for CrewAI 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
Geminifrom crewai import Agent, Task, Crew
agent = Agent(
role="EBI Proteins API Specialist",
goal="Help users interact with EBI Proteins API effectively",
backstory=(
"You are an expert at leveraging EBI Proteins API tools "
"for automation and data analysis."
),
# Your Vinkius token. get it at cloud.vinkius.com
mcps=["https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"],
)
task = Task(
description=(
"Explore all available tools in EBI Proteins API "
"and summarize their capabilities."
),
agent=agent,
expected_output=(
"A detailed summary of 16 available tools "
"and what they can do."
),
)
crew = Crew(agents=[agent], tasks=[task])
result = crew.kickoff()
print(result)
* 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.
When paired with CrewAI, EBI Proteins API becomes a first-class tool in your multi-agent workflows. Each agent in the crew can call EBI Proteins API tools autonomously, one agent queries data, another analyzes results, a third compiles reports, all orchestrated through Vinkius with zero configuration overhead.
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 CrewAI 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 CrewAI
When CrewAI 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 CrewAI via MCP
Follow these steps to wire EBI Proteins API into CrewAI. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install CrewAI
pip install crewaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.comCustomize the agent
role, goal, and backstory to fit your use caseRun the crew
python crew.py. CrewAI auto-discovers 16 tools from EBI Proteins APIWhy Use CrewAI with the EBI Proteins API MCP Server
CrewAI Multi-Agent Orchestration Framework provides unique advantages when paired with EBI Proteins API through the Model Context Protocol.
Multi-agent collaboration lets you decompose complex workflows into specialized roles, one agent researches, another analyzes, a third generates reports, each with access to MCP tools
CrewAI's native MCP integration requires zero adapter code: pass Vinkius Edge URL directly in the `mcps` parameter and agents auto-discover every available tool at runtime
Built-in task delegation and shared memory mean agents can pass context between steps without manual state management, enabling multi-hop reasoning across tool calls
Sequential and hierarchical crew patterns map naturally to real-world workflows: enumerate subdomains → analyze DNS history → check WHOIS records → compile findings into actionable reports
EBI Proteins API + CrewAI Use Cases
Practical scenarios where CrewAI combined with the EBI Proteins API MCP Server delivers measurable value.
Automated multi-step research: a reconnaissance agent queries EBI Proteins API for raw data, then a second analyst agent cross-references findings and flags anomalies. all without human handoff
Scheduled intelligence reports: set up a crew that periodically queries EBI Proteins API, analyzes trends over time, and generates executive briefings in markdown or PDF format
Multi-source enrichment pipelines: chain EBI Proteins API tools with other MCP servers in the same crew, letting agents correlate data across multiple providers in a single workflow
Compliance and audit automation: a compliance agent queries EBI Proteins API against predefined policy rules, generates deviation reports, and routes findings to the appropriate team
Example Prompts for EBI Proteins API in CrewAI
Ready-to-use prompts you can give your CrewAI 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 CrewAI
Common issues when connecting EBI Proteins API to CrewAI through Vinkius, and how to resolve them.
MCP tools not discovered
Agent not using tools
Timeout errors
Rate limiting or 429 errors
EBI Proteins API + CrewAI FAQ
Common questions about integrating EBI Proteins API MCP Server with CrewAI.
How does CrewAI discover and connect to MCP tools?
tools/list method. This means tools are always fresh and reflect the server's current capabilities. No tool schemas need to be hardcoded.Can different agents in the same crew use different MCP servers?
mcps list, so you can assign specific servers to specific roles. For example, a reconnaissance agent might use a domain intelligence server while an analysis agent uses a vulnerability database server.What happens when an MCP tool call fails during a crew run?
Can CrewAI agents call multiple MCP tools in parallel?
process=Process.parallel, each calling different MCP tools concurrently. This is ideal for workflows where separate data sources need to be queried simultaneously.Can I run CrewAI crews on a schedule (cron)?
crew.kickoff() method runs synchronously by default, making it straightforward to integrate into existing pipelines.Explore More MCP Servers
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