EBI PDBe MCP Server for Google ADKGive Google ADK instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersGoogle Agent Development Kit (ADK) is Google's framework for building production AI agents. Add EBI PDBe as an MCP tool provider through Vinkius and your ADK agents can call every tool with full schema introspection.
Ask AI about this MCP Server for Google ADK
The EBI PDBe MCP Server for Google ADK 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 google.adk.agents import Agent
from google.adk.tools.mcp_tool import McpToolset
from google.adk.tools.mcp_tool.mcp_session_manager import (
StreamableHTTPConnectionParams,
)
# Your Vinkius token. get it at cloud.vinkius.com
mcp_tools = McpToolset(
connection_params=StreamableHTTPConnectionParams(
url="https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
)
)
agent = Agent(
model="gemini-2.5-pro",
name="ebi_pdbe_agent",
instruction=(
"You help users interact with EBI PDBe "
"using 16 available tools."
),
tools=[mcp_tools],
)
* 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 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.
Google ADK natively supports EBI PDBe as an MCP tool provider. declare Vinkius Edge URL and the framework handles discovery, validation, and execution automatically. Combine 16 tools with Gemini's long-context reasoning for complex multi-tool workflows, with production-ready session management and evaluation built in.
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 Google ADK 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 Google ADK
When Google ADK 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 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 binding sites on EBI PDBe
Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions
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 experiment on EBI PDBe
Get experimental method details for a structure
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 modified residues on EBI PDBe
Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides
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 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 publications on EBI PDBe
Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs
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 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 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 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 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 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 Google ADK via MCP
Follow these steps to wire EBI PDBe into Google ADK. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install Google ADK
pip install google-adkReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenCreate the agent
Explore tools
Why Use Google ADK with the EBI PDBe MCP Server
Google ADK provides unique advantages when paired with EBI PDBe through the Model Context Protocol.
Google ADK natively supports MCP tool servers. declare a tool provider and the framework handles discovery, validation, and execution
Built on Gemini models, ADK provides long-context reasoning ideal for complex multi-tool workflows with EBI PDBe
Production-ready features like session management, evaluation, and deployment come built-in. not bolted on
Seamless integration with Google Cloud services means you can combine EBI PDBe tools with BigQuery, Vertex AI, and Cloud Functions
EBI PDBe + Google ADK Use Cases
Practical scenarios where Google ADK combined with the EBI PDBe MCP Server delivers measurable value.
Enterprise data agents: ADK agents query EBI PDBe and cross-reference results with internal databases for comprehensive analysis
Multi-modal workflows: combine EBI PDBe tool responses with Gemini's vision and language capabilities in a single agent
Automated compliance checks: schedule ADK agents to query EBI PDBe regularly and flag policy violations or configuration drift
Internal tool platforms: build self-service agent platforms where teams connect their own MCP servers including EBI PDBe
Example Prompts for EBI PDBe in Google ADK
Ready-to-use prompts you can give your Google ADK 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 Google ADK
Common issues when connecting EBI PDBe to Google ADK through Vinkius, and how to resolve them.
McpToolset not found
pip install --upgrade google-adkEBI PDBe + Google ADK FAQ
Common questions about integrating EBI PDBe MCP Server with Google ADK.
How does Google ADK connect to MCP servers?
Can ADK agents use multiple MCP servers?
Which Gemini models work best with MCP tools?
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