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DimensionNeo4j Cypher MCP ServerAn MCP server for running Cypher queries against a Neo4j database.MCP ClickHouseConnect ClickHouse to your AI assistantsChEMBL MCP ServerUnofficial MCP server providing advanced access to the ChEMBL chemical database
FMRS56 / 100 · C79 / 100 · B75 / 100 · B
Reliability8 / 2012 / 2012 / 20
Security and permissions11 / 2018 / 2016 / 20
Maintenance13 / 2017 / 2014 / 20
Documentation12 / 2017 / 2018 / 20
Setup experience12 / 2015 / 2015 / 20
Best for
  • Developers who already run a Neo4j instance and want to query it in natural language
  • Users of MCP clients such as Claude Desktop, VS Code, Cursor, Windsurf, or Gemini CLI
  • Teams looking to connect a graph database to LLM workflows
  • Users comfortable with lab-stage experimental features and self-supported maintenance
  • Teams already using ClickHouse who want AI assistants to access data directly.
  • Scenarios requiring fast, read-only data queries and schema exploration.
  • Drug discovery and computational chemistry researchers
  • Bioinformatics teams needing ChEMBL data through AI assistants
  • Developers comfortable with Node.js or Docker
Not for
  • Production users who need official product support, SLAs, or backwards compatibility guarantees
  • Neo4j instances where the APOC plugin cannot be installed or enabled (schema inspection will not work)
  • Users who only want the officially supported Neo4j MCP server
  • Users without an accessible Neo4j instance or database credentials
  • Scenarios requiring write access to the database without explicit opt-in.
  • Production environments with stringent security requirements that avoid default permission settings.
  • Production settings requiring official ChEMBL support (this is unofficial)
  • Users without a Node.js or Docker environment
  • General database tasks unrelated to ChEMBL
Required permissions
  • Read the configured Neo4j database and its schema
  • Execute read and write Cypher queries on the configured Neo4j database
  • Access Neo4j credentials, including NEO4J_URI, NEO4J_USERNAME, and the sensitive NEO4J_PASSWORD
  • Requires read-only access to ClickHouse database (default).
  • Optional: write access via CLICKHOUSE_ALLOW_WRITE_ACCESS.
  • Optional: destructive operations via CLICKHOUSE_ALLOW_DROP.
  • Outbound network access to https://www.ebi.ac.uk/chembl/api/data
  • Read-only access to public API data; no authentication credentials required
Risks and side effects
  • This is an experimental Neo4j Labs project with no SLAs or backwards compatibility guarantees, and it may change between versions
  • Write Cypher queries can be executed by default, potentially modifying or deleting data in the database
  • NEO4J_PASSWORD is sensitive and can leak if misconfigured
  • The server is not officially supported by the Neo4j product team
  • Deploying in HTTP/SSE mode on a network may expose the endpoint to unauthorized access
  • If write access is enabled, AI might make unintended modifications.
  • If DROP access is enabled, data deletion could occur accidentally.
  • Credentials may be exposed via environment variables.
  • Unofficial project with license marked NOASSERTION (README claims MIT); verify licensing yourself
  • Data accuracy depends on the ChEMBL REST API and the server's parsing may contain defects
  • 30-second request timeouts may constrain large batch queries
  • README inconsistency on tool count (22 vs 27) raises documentation reliability concerns
Supported clientsClaude Desktop, VS Code, Cursor, Windsurf, Gemini CLIClaude DesktopClaude Desktop
Tools0427