PDBe-MCP-Servers
PDBe-MCP-Servers is an MCP server, listed under databases. It reaches neo4j. It needs NEO4J_PASSWORD to authenticate. Its repository has 43 GitHub stars and is licensed under Apache-2.0; we last read it on 2026-10-22.
PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.
Install
MCP servers are packaged differently from each other -- some run via npx, some as a Docker image, some as a plain script you clone and run. PDBe-MCP-Servers’s own README did not state one plainly enough for this page to quote it rather than guess, so it will not guess. The repository below states it.
What it reaches, and what it needs
Maintenance
PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.
PDBe-MCP-Servers compared with similar servers
| Server | Reaches | Needs | Stars | Last update | Licence |
|---|---|---|---|---|---|
| PDBe-MCP-Servers (this page) | neo4j | NEO4J_PASSWORD | 43 | 2026-10-22 | Apache-2.0 |
| CodeGraphContext | neo4j(1 shared) | NEO4J_PASSWORD | 4,360 | 2026-10-22 | MIT |
| atlas-mcp-server | neo4j(1 shared) | MCP_AUTH_SECRET_KEY, NEO4J_PASSWORD | 478 | 2025-07-22 | Apache-2.0 |
| mcp | neo4j(1 shared) | NEO4J_MCP_PASSWORD | 300 | 2026-10-22 | NOASSERTION |
| mcp-neo4j-memory-server | neo4j(1 shared) | NEO4J_PASSWORD | 23 | 2025-03-15 | MIT |
| claude-code-memory | neo4j(1 shared) | NEO4J_PASSWORD | 11 | 2025-06-28 | — |
Ranked by services in common with PDBe-MCP-Servers, then by stars. Figures are from each repository when we last read it.
Common questions about PDBe-MCP-Servers
- What does PDBe-MCP-Servers do?
- PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.
- How do I install PDBe-MCP-Servers?
- Its README did not state an install command plainly enough for us to quote one, so we do not guess. The repository has the instructions: https://github.com/PDBeurope/PDBe-MCP-Servers
- What does PDBe-MCP-Servers connect to, and what does it need?
- It reaches neo4j. The credentials we found in its source are NEO4J_PASSWORD.
- Is PDBe-MCP-Servers official and is it maintained?
- We found nothing naming it as a vendor’s official server. Its repository has 43 GitHub stars and its state in our directory is listed. Its last commit we recorded was on 2026-10-22.
- What licence does PDBe-MCP-Servers use?
- The repository declares the Apache-2.0 licence.
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