EBI PDBe MCP Server for LangChainGive LangChain instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersLangChain is the leading Python framework for composable LLM applications. Connect EBI PDBe through Vinkius and LangChain agents can call every tool natively. combine them with retrievers, memory, and output parsers for sophisticated AI pipelines.
Ask AI about this MCP Server for LangChain
The EBI PDBe MCP Server for LangChain 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
Geminiimport asyncio
from langchain_mcp_adapters.client import MultiServerMCPClient
from langchain_openai import ChatOpenAI
from langgraph.prebuilt import create_react_agent
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
async with MultiServerMCPClient({
"ebi-pdbe": {
"transport": "streamable_http",
"url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp",
}
}) as client:
tools = client.get_tools()
agent = create_react_agent(
ChatOpenAI(model="gpt-4o"),
tools,
)
response = await agent.ainvoke({
"messages": [{
"role": "user",
"content": "Using EBI PDBe, show me what tools are available.",
}]
})
print(response["messages"][-1].content)
asyncio.run(main())
* 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.
LangChain's ecosystem of 500+ components combines seamlessly with EBI PDBe through native MCP adapters. Connect 16 tools via Vinkius and use ReAct agents, Plan-and-Execute strategies, or custom agent architectures. with LangSmith tracing giving full visibility into every tool call, latency, and token cost.
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 LangChain 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 LangChain
When LangChain 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 LangChain via MCP
Follow these steps to wire EBI PDBe into LangChain. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install dependencies
pip install langchain langchain-mcp-adapters langgraph langchain-openaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
python agent.pyExplore tools
Why Use LangChain with the EBI PDBe MCP Server
LangChain provides unique advantages when paired with EBI PDBe through the Model Context Protocol.
The largest ecosystem of integrations, chains, and agents. combine EBI PDBe MCP tools with 500+ LangChain components
Agent architecture supports ReAct, Plan-and-Execute, and custom strategies with full MCP tool access at every step
LangSmith tracing gives you complete visibility into tool calls, latencies, and token usage for production debugging
Memory and conversation persistence let agents maintain context across EBI PDBe queries for multi-turn workflows
EBI PDBe + LangChain Use Cases
Practical scenarios where LangChain combined with the EBI PDBe MCP Server delivers measurable value.
RAG with live data: combine EBI PDBe tool results with vector store retrievals for answers grounded in both real-time and historical data
Autonomous research agents: LangChain agents query EBI PDBe, synthesize findings, and generate comprehensive research reports
Multi-tool orchestration: chain EBI PDBe tools with web scrapers, databases, and calculators in a single agent run
Production monitoring: use LangSmith to trace every EBI PDBe tool call, measure latency, and optimize your agent's performance
Example Prompts for EBI PDBe in LangChain
Ready-to-use prompts you can give your LangChain 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 LangChain
Common issues when connecting EBI PDBe to LangChain through Vinkius, and how to resolve them.
MultiServerMCPClient not found
pip install langchain-mcp-adaptersEBI PDBe + LangChain FAQ
Common questions about integrating EBI PDBe MCP Server with LangChain.
How does LangChain connect to MCP servers?
langchain-mcp-adapters to create an MCP client. LangChain discovers all tools and wraps them as native LangChain tools compatible with any agent type.Which LangChain agent types work with MCP?
Can I trace MCP tool calls in LangSmith?
Explore More MCP Servers
View all →
HTML XSS Sanitizer
1 toolsProtect your database from malicious code. Clean and sanitize user-generated HTML payloads instantly local.
Crypto Hash Engine
1 toolsSign API requests and Webhooks deterministically. Instantly generate mathematical HMAC, SHA-256, or MD5 hashes without AI hallucinations.
Arize AI
10 toolsAutomate LLM and ML observability via Arize — monitor models, track telemetry, run evaluations, and analyze data drift directly from any AI agent.
YAML Parser Engine
1 toolsConvert YAML to JSON and JSON to YAML with absolute precision — including anchors, aliases, and multi-document support. The engine behind Kubernetes, GitHub Actions, and Docker Compose config processing. 30M+ weekly downloads.