EBI PDBe MCP Server for CursorGive Cursor 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

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Cursor is an AI-first code editor built on VS Code that integrates LLM-powered coding assistance directly into the development workflow. Its Agent mode enables autonomous multi-step coding tasks, and MCP support lets agents access external data sources and APIs during code generation.

Ask AI about this MCP Server for Cursor

Open in ChatGPT Open in Claude Open in Perplexity

The EBI PDBe MCP Server for Cursor 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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+ other MCP clients

Classic Setup·json

{
  "mcpServers": {
    "ebi-pdbe": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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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.

Cursor's Agent mode turns EBI PDBe into an in-editor superpower. Ask Cursor to generate code using live data from EBI PDBe and it fetches, processes, and writes. all in a single agentic loop. 16 tools appear alongside file editing and terminal access, creating a unified development environment grounded in real-time information.

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 Cursor 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 Cursor

When Cursor 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 Cursor via MCP

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

Open MCP Settings

Press Cmd+Shift+P (macOS) or Ctrl+Shift+P (Windows/Linux) → search "MCP Settings"

Add the server config

Paste the JSON configuration above into the mcp.json file that opens

Save the file

Cursor will automatically detect the new MCP server

Start using EBI PDBe

Open Agent mode in chat and ask: "Using EBI PDBe, help me...". 16 tools available

Why Use Cursor with the EBI PDBe MCP Server

Cursor AI Code Editor provides unique advantages when paired with EBI PDBe through the Model Context Protocol.

Agent mode turns Cursor into an autonomous coding assistant that can read files, run commands, and call MCP tools without switching context

Cursor's Composer feature can generate entire files using real-time data fetched through MCP. no copy-pasting from external dashboards

MCP tools appear alongside built-in tools like file reading and terminal access, creating a unified agentic environment

VS Code extension compatibility means your existing workflow, keybindings, and extensions all work alongside MCP tools

EBI PDBe + Cursor Use Cases

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

Code generation with live data: ask Cursor to generate a security report module using live DNS and subdomain data fetched through MCP

Automated documentation: have Cursor query your API's tool schemas and generate TypeScript interfaces or OpenAPI specs automatically

Infrastructure-as-code: Cursor can fetch domain configurations and generate corresponding Terraform or CloudFormation templates

Test scaffolding: ask Cursor to pull real API responses via MCP and generate unit test fixtures from actual data

Example Prompts for EBI PDBe in Cursor

Ready-to-use prompts you can give your Cursor 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 Cursor

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

Tools not appearing in Cursor

Ensure you are in Agent mode (not Ask mode). MCP tools only work in Agent mode.

Server shows as disconnected

Check Settings → Features → MCP and verify the server status. Try clicking the refresh button.

EBI PDBe + Cursor FAQ

Common questions about integrating EBI PDBe MCP Server with Cursor.

What is Agent mode and why does it matter for MCP?

Agent mode is Cursor's autonomous execution mode where the AI can perform multi-step tasks: reading files, editing code, running terminal commands, and calling MCP tools. Without Agent mode, Cursor operates in a simpler ask-and-answer mode that doesn't support tool calling. Always ensure you're in Agent mode when working with MCP servers.

Where does Cursor store MCP configuration?

Cursor looks for MCP server configurations in a mcp.json file. You can configure servers at the project level (.cursor/mcp.json in your project root) or globally (~/.cursor/mcp.json). Project-level configs take precedence.

Can Cursor use MCP tools in inline edits?

No. MCP tools are only available in Agent mode through the chat panel. Inline completions and Tab suggestions do not trigger MCP tool calls. This is by design. tool calls require user visibility and approval.

How do I verify MCP tools are loaded?

Open Settings → Features → MCP and look for your server name. A green indicator means the server is connected. You can also check Agent mode's available tools by clicking the tools dropdown in the chat panel.