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DimensionPubChem MCP ServerSearch the PubChem chemical database for compounds, properties, safety data, bioactivity, and cross-references via MCP. STDIO or Streamable HTTP.MCP ClickHouseConnect ClickHouse to your AI assistantsChEMBL MCP ServerUnofficial MCP server providing advanced access to the ChEMBL chemical database
FMRS59 / 100 · C79 / 100 · B75 / 100 · B
Reliability10 / 2012 / 2012 / 20
Security and permissions12 / 2018 / 2016 / 20
Maintenance10 / 2017 / 2014 / 20
Documentation14 / 2017 / 2018 / 20
Setup experience13 / 2015 / 2015 / 20
Best for
  • Researchers and developers integrating chemical database queries into LLM-driven tools.
  • Those preferring a public hosted endpoint or self-hosting their own MCP server.
  • 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
  • Clinical applications requiring rich drug interaction coverage (the report covers mostly approved drugs).
  • Use cases needing write access or data ingestion (the server is read-only).
  • 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
  • Reads PubChem public APIs; no authentication required.
  • Optional environment variables for logging/HTTP configuration.
  • 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
  • The public hosted instance's availability may vary (not officially affiliated).
  • Deep pagination may incur additional upstream requests and potential rate limits.
  • Error handling depends on remote service reliability.
  • 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, Cursor, VS CodeClaude DesktopClaude Desktop
Tools10427