Integrate EBI PDBe with Claude, Cursor, Chatbots & AI Agents MCP Server
GDPR Free for SubscribersCompatible with every major AI agent and IDE
GeminiGet 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
Security & Code Integrity Audit
Every tool in the EBI PDBe MCP Server is continuously audited by the Vinkius Security Engine. We guarantee zero-trust payload isolation, strict data boundaries, and deterministic execution for enterprise-grade AI agents.
How Vinkius protects your data
Is there a risk of the AI "going crazy" and deleting important company data?
No. With Vinkius, the AI operates on "rails". It can only make the exact moves you authorized in the tool's settings. It cannot invent routes, access other networks in your company, or decide to delete random files. If the action isn't in the approved catalog, the attempt is blocked instantly.
Can I audit what my AI agents are doing with this integration?
Yes, Vinkius provides an immutable, HMAC-chained audit log. Every tool execution, payload, and response is tracked in real-time on your dashboard, giving you complete visibility into your agent's actions.
What if the AI ends up reading customer data or confidential information?
We have a built-in digital "bodyguard" called DLP (Data Loss Prevention). If a tool fetches data and the response contains social security numbers, credit cards, or personal customer info, Vinkius magically blocks and erases that information before it is delivered to the AI. The AI works only with what is strictly necessary, and your sensitive data never leaks.
Do I need an API key?
No. The PDBe API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.
How Chatbots Interact with EBI PDBe
The EBI PDBe integration provides comprehensive execution endpoints, allowing AI models to orchestrate tasks reliably.
AI-Driven pdb Workflows
The EBI PDBe server exposes documented endpoints for pdb. This allows ChatGPT and Cursor to interact with the unthinkable APIs seamlessly.
Intelligent protein structure Management
The EBI PDBe integration allows Cursor and ChatGPT to securely fetch protein structure data. It handles the API requests required for the unthinkable operations.
EBI PDBe. Runs on everything.
From IDE to framework. Every connection governed by Vinkius.
Anthropic's native desktop app for Claude with built-in MCP support.
AI-first code editor with integrated LLM-powered coding assistance.
GitHub Copilot in VS Code with Agent mode and MCP support.
Purpose-built IDE for agentic AI coding workflows.
Autonomous AI coding agent that runs inside VS Code.
Anthropic's agentic CLI for terminal-first development.
Python SDK for building production-grade OpenAI agent workflows.
Google's framework for building production AI agents.
Type-safe agent development for Python with first-class MCP support.
TypeScript toolkit for building AI-powered web applications.
TypeScript-native agent framework for modern web stacks.
Python framework for orchestrating collaborative AI agent crews.
Leading Python framework for composable LLM applications.
Data-aware AI agent framework for structured and unstructured sources.
Microsoft's framework for multi-agent collaborative conversations.
Explore More MCP Servers
View all →
Alpha Vantage
13 toolsAccess stock market data via Alpha Vantage — get real-time quotes, time series, technical indicators and crypto/forex data from any AI agent.
Cheddar
8 toolsManage usage-based billing and subscriptions via Cheddar — track usage, monitor invoices, and manage customers directly from any AI agent.
Eurostat Trade — EU International Commerce
5 toolsEU international trade data: imports and exports by partner country and product classification (SITC), industrial production index, retail trade volume, and services sector statistics for all 27 EU member states.
Monday.com (Work Management & CRM)
9 toolsManage work via Monday.com — list project boards, track task items, and audit team workspaces.