EBI PDBe MCP Server for LlamaIndexGive LlamaIndex instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersLlamaIndex specializes in data-aware AI agents that connect LLMs to structured and unstructured sources. Add EBI PDBe as an MCP tool provider through Vinkius and your agents can query, analyze, and act on live data alongside your existing indexes.
Ask AI about this MCP Server for LlamaIndex
The EBI PDBe MCP Server for LlamaIndex 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 llama_index.tools.mcp import BasicMCPClient, McpToolSpec
from llama_index.core.agent.workflow import FunctionAgent
from llama_index.llms.openai import OpenAI
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
mcp_client = BasicMCPClient("https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")
mcp_tool_spec = McpToolSpec(client=mcp_client)
tools = await mcp_tool_spec.to_tool_list_async()
agent = FunctionAgent(
tools=tools,
llm=OpenAI(model="gpt-4o"),
system_prompt=(
"You are an assistant with access to EBI PDBe. "
"You have 16 tools available."
),
)
response = await agent.run(
"What tools are available in EBI PDBe?"
)
print(response)
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.
LlamaIndex agents combine EBI PDBe tool responses with indexed documents for comprehensive, grounded answers. Connect 16 tools through Vinkius and query live data alongside vector stores and SQL databases in a single turn. ideal for hybrid search, data enrichment, and analytical workflows.
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 LlamaIndex 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 LlamaIndex
When LlamaIndex 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 LlamaIndex via MCP
Follow these steps to wire EBI PDBe into LlamaIndex. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install dependencies
pip install llama-index-tools-mcp llama-index-llms-openaiReplace the token
[YOUR_TOKEN_HERE] with your Vinkius tokenRun the agent
agent.py and run: python agent.pyExplore tools
Why Use LlamaIndex with the EBI PDBe MCP Server
LlamaIndex provides unique advantages when paired with EBI PDBe through the Model Context Protocol.
Data-first architecture: LlamaIndex agents combine EBI PDBe tool responses with indexed documents for comprehensive, grounded answers
Query pipeline framework lets you chain EBI PDBe tool calls with transformations, filters, and re-rankers in a typed pipeline
Multi-source reasoning: agents can query EBI PDBe, a vector store, and a SQL database in a single turn and synthesize results
Observability integrations show exactly what EBI PDBe tools were called, what data was returned, and how it influenced the final answer
EBI PDBe + LlamaIndex Use Cases
Practical scenarios where LlamaIndex combined with the EBI PDBe MCP Server delivers measurable value.
Hybrid search: combine EBI PDBe real-time data with embedded document indexes for answers that are both current and comprehensive
Data enrichment: query EBI PDBe to augment indexed data with live information before generating user-facing responses
Knowledge base agents: build agents that maintain and update knowledge bases by periodically querying EBI PDBe for fresh data
Analytical workflows: chain EBI PDBe queries with LlamaIndex's data connectors to build multi-source analytical reports
Example Prompts for EBI PDBe in LlamaIndex
Ready-to-use prompts you can give your LlamaIndex 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 LlamaIndex
Common issues when connecting EBI PDBe to LlamaIndex through Vinkius, and how to resolve them.
BasicMCPClient not found
pip install llama-index-tools-mcpEBI PDBe + LlamaIndex FAQ
Common questions about integrating EBI PDBe MCP Server with LlamaIndex.
How does LlamaIndex connect to MCP servers?
Can I combine MCP tools with vector stores?
Does LlamaIndex support async MCP calls?
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