Nullary

Nullary vs. ChEMBL

TLDR

  • ChEMBL is the canonical bioactivity database for medicinal chemistry, maintained by EMBL-EBI since 2009
  • Nullary aggregates ChEMBL plus 24+ other public databases (including ChEMBL itself) and exposes them via MCP server with unified schema
  • ChEMBL is free, comprehensive for small molecules, and the right choice if you need bulk activity data or complete history of a target's chemistry
  • Nullary is the right choice if you want cross-modality queries (small molecules + CRISPR + antibodies + clinical trials together), MCP-native integration, or real-time alerts on new failures

What each does

ChEMBL is a manually curated database of bioactive molecules. Comprehensive coverage of small-molecule activity data extracted from medicinal chemistry literature. Free, public, well-maintained. The reference standard for compound activity data.

Nullary is a unified MCP-queryable layer over negative results across drug discovery modalities. Uses ChEMBL as one of 25+ sources alongside DepMap, FLAb, PROTAC-DB, ClinicalTrials.gov, and others.

When to use ChEMBL directly

  • You need bulk download of all known activity data
  • You're working in small-molecule chemistry only
  • You need fields that ChEMBL has but Nullary doesn't surface (e.g., assay quality metadata, full SAR tables)
  • You're integrating into an existing pipeline that already uses ChEMBL

When to use Nullary

  • You want cross-modality queries: “everything tried against this target across small molecules, CRISPR, antibodies, PROTACs, clinical trials”
  • You want MCP-native access from Claude Desktop, Cursor, Claude Code
  • You want alerts when new failures appear in your areas of interest
  • You want analytics on top of the raw data (target tractability, modality coverage maps, failure timelines — Premium tier)
  • You're building agent workflows that need structured negative-results data

Data overlap

Nullary's small-molecule modality includes the inactive subset of ChEMBL (~3-5M records). Every Nullary record sourced from ChEMBL is cited as such with full provenance. Nullary respects ChEMBL's CC-BY-SA 3.0 license; ChEMBL-derived records carry share-alike requirements.

Pricing

ChEMBL is free. Nullary's free tier covers all 7 modalities with usable rate limits. Nullary paid tiers ($49+/mo) add alerts and analytics that ChEMBL doesn't provide.

Bottom line

Use both. ChEMBL for direct bulk access to medicinal chemistry data. Nullary for cross-modality queries, MCP integration, alerts, and analytics. They're complementary, not competitive.