EBI PDBe MCP Server for CrewAIGive CrewAI instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more

Name: EBI PDBe
Price: 29 USD
Availability: InStock
Rating: 5.0 (1 reviews)
Author: Vinkius

GDPR Free for Subscribers

Connect your CrewAI agents to EBI PDBe through Vinkius, pass the Edge URL in the `mcps` parameter and every EBI PDBe tool is auto-discovered at runtime. No credentials to manage, no infrastructure to maintain.

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The EBI PDBe 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.

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python

from crewai import Agent, Task, Crew

agent = Agent(
    role="EBI PDBe Specialist",
    goal="Help users interact with EBI PDBe effectively",
    backstory=(
        "You are an expert at leveraging EBI PDBe 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 PDBe "
        "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)

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About EBI PDBe MCP Server

Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.

When paired with CrewAI, EBI PDBe becomes a first-class tool in your multi-agent workflows. Each agent in the crew can call EBI PDBe 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

Structure Summaries — Get titles, authors, deposition dates, resolution, and experimental methods for any PDB entry
Molecular Entities — Retrieve protein chains, nucleic acids, ligands, their sequences, source organisms, and gene names
Binding Sites & Ligands — Access ligand binding pocket residues, small molecule ligands with formulas and weights
Quality Assessment — Check resolution, R-factors, and overall quality scores for structure reliability
UniProt Mappings — Map between UniProt sequence positions and PDB residue numbers
Biological Assemblies — Understand quaternary structure — monomer, dimer, tetramer, or higher-order complexes
Structure Search — Full-text Solr search across 200+ PDB metadata fields
Publications — Find primary citations, PubMed IDs, and related structural studies

The EBI PDBe 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 PDBe tools available for CrewAI

When CrewAI connects to EBI PDBe through Vinkius, your AI agent gets direct access to every tool listed below — spanning pdb, protein-structure, 3d-structures, 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

Get assemblies on EBI PDBe

Returns assembly IDs, composition (which entities and how many copies), preferred assembly flag, and form description. Critical for understanding whether a protein functions as a monomer, dimer, tetramer, or higher-order complex. Get biological assembly information (quaternary structure)

get

Get binding sites on EBI PDBe

Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions

get

Get cofactors on EBI PDBe

Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations

get

Get experiment on EBI PDBe

Get experimental method details for a structure

get

Get ligand monomers on EBI PDBe

Returns chemical component IDs, names, molecular formulas, molecular weights, and their chain/residue positions. Essential for drug discovery and understanding protein-small molecule interactions. Get small molecule ligands bound in the structure

get

Get modified residues on EBI PDBe

Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides

get

Get molecules on EBI PDBe

Returns entity IDs, molecule types, names, chain assignments, sequence lengths, molecular weights, source organisms, and gene names. Get molecular entities (chains, polymers) in a structure

get

Get mutated residues on EBI PDBe

Shows the original residue, mutated residue, chain, and position. Essential for understanding how the crystallized construct differs from the native protein. Get engineered mutations vs. wild-type sequence

get

Get publications on EBI PDBe

Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs

get

Get quality scores on EBI PDBe

The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure

get

Get related entries on EBI PDBe

Useful for discovering alternative conformations, mutants, or complexes of the same protein that have been structurally characterized. Get related PDB entries citing the same publications

get

Get residue listing on EBI PDBe

Shows residue names, numbers (both PDB and author numbering), organized by entity and chain. Returns a sample of the first 20 residues per chain for efficiency. Get full residue-level inventory per chain

get

Get secondary structure on EBI PDBe

Shows the count of helices and strands per chain, organized by molecular entity. Essential for understanding protein fold topology. Get helix, sheet, and coil assignments per residue

get

Get summary on EBI PDBe

Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution

get

Get uniprot mapping on EBI PDBe

Returns UniProt accessions, chain assignments, and start/end position mappings. Essential for cross-referencing between protein sequence databases and 3D structural data. Get UniProt to PDB residue mappings

Search structures on EBI PDBe

Use natural language queries like "insulin receptor kinase", "SARS-CoV-2 spike protein", "cryo-EM resolution<3", or specific organism names. Returns PDB IDs, titles, methods, resolutions, and organisms. Search PDB structures with full-text queries

Connect EBI PDBe to CrewAI via MCP

Follow these steps to wire EBI PDBe into CrewAI. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Install CrewAI

Run pip install crewai

Replace the token

Replace [YOUR_TOKEN_HERE] with your Vinkius token from cloud.vinkius.com

Customize the agent

Adjust the role, goal, and backstory to fit your use case

Run the crew

Run python crew.py. CrewAI auto-discovers 16 tools from EBI PDBe

Why Use CrewAI with the EBI PDBe MCP Server

CrewAI Multi-Agent Orchestration Framework provides unique advantages when paired with EBI PDBe 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 PDBe + CrewAI Use Cases

Practical scenarios where CrewAI combined with the EBI PDBe MCP Server delivers measurable value.

Automated multi-step research: a reconnaissance agent queries EBI PDBe 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 PDBe, analyzes trends over time, and generates executive briefings in markdown or PDF format

Multi-source enrichment pipelines: chain EBI PDBe 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 PDBe against predefined policy rules, generates deviation reports, and routes findings to the appropriate team

Example Prompts for EBI PDBe in CrewAI

Ready-to-use prompts you can give your CrewAI agent to start working with EBI PDBe immediately.

"Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)."

"What ligands are bound in the hemoglobin structure 4hhb?"

"Search for cryo-EM structures of ribosome complexes."

Troubleshooting EBI PDBe MCP Server with CrewAI

Common issues when connecting EBI PDBe to CrewAI through Vinkius, and how to resolve them.

MCP tools not discovered

Ensure the Edge URL is correct. CrewAI connects lazily when the crew starts. check console output.

Agent not using tools

Make the task description specific. Instead of "do something", say "Use the available tools to list contacts".

Timeout errors

CrewAI has a 10s connection timeout by default. Ensure your network can reach the Edge URL.

Rate limiting or 429 errors

Vinkius enforces per-token rate limits. Check your subscription tier and request quota in the dashboard. Upgrade if you need higher throughput.

EBI PDBe + CrewAI FAQ

Common questions about integrating EBI PDBe MCP Server with CrewAI.

How does CrewAI discover and connect to MCP tools?

CrewAI connects to MCP servers lazily. when the crew starts, each agent resolves its MCP URLs and fetches the tool catalog via the standard 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?

Yes. Each agent has its own 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?

CrewAI wraps tool failures as context for the agent. The LLM receives the error message and can decide to retry with different parameters, fall back to a different tool, or mark the task as partially complete. This resilience is critical for production workflows.

Can CrewAI agents call multiple MCP tools in parallel?

CrewAI agents execute tool calls sequentially within a single reasoning step. However, you can run multiple agents in parallel using 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)?

Yes. CrewAI crews are standard Python scripts, so you can invoke them via cron, Airflow, Celery, or any task scheduler. The crew.kickoff() method runs synchronously by default, making it straightforward to integrate into existing pipelines.

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