Nullary MCP Server

Negative results intelligence for drug discovery — over the Model Context Protocol.

Nullary is a hosted MCP server that lets AI agents query measured negative results from drug discovery: inactive compounds, failed selectivity panels, terminated clinical trials, failed CRISPR screens, antibody developability failures, and more — each result carrying full provenance (source database, DOI/PMID, license).

This repository documents the public MCP interface. The server is hosted; the data pipeline and application code are maintained separately.

Connect

Nullary is a remote MCP server (streamable-HTTP) — nothing to install, no API key:

https://mcp.nullary.ai/mcp

Claude Code / generic MCP client

{
  "mcpServers": {
    "nullary": {
      "url": "https://mcp.nullary.ai/mcp"
    }
  }
}

Cursor

Settings → MCP → Add new MCP server → paste the URL above (transport: streamable-HTTP).

Claude Desktop

Settings → Connectors → Add custom connector → URL https://mcp.nullary.ai/mcp.

What you can ask

• "What's failed against EGFR?" — failed compounds, trials, and screens for a target, across modalities
• "Which kinase inhibitors were inactive in ChEMBL?"
• "Show terminated Phase 2 oncology trials and why they stopped"
• "Failed CRISPR knockouts for TP53"

Tools are organized by modality (small molecule, CRISPR, antibody, peptide, PROTAC, clinical trial, …); every response cites its source.

Tools

The server exposes 35 tools — served live via the MCP tools/list method. Full JSON Schemas (inputs per tool) are in tools.json. Tools span the seven modalities plus cross-modality history, compound/provenance lookups, and the Layer-1 model registry.

Tool	Description
search_inactive_compounds	Inactive small-molecule compound-target pairs.
search_failed_selectivity	Small molecules that failed selectivity.
search_admet_failures	Small-molecule ADMET failures.
search_failed_guides	Failed/ineffective CRISPR guides.
search_failed_essentiality_screens	Non-dependency / failed essentiality screens.
search_ancestry_specific_failures	Ancestry-specific CRISPR failures.
search_developability_failures	Antibody developability failures.
search_failed_clinical_antibodies	Discontinued/terminated clinical antibodies.
search_failed_peptide_therapeutics	Failed peptide therapeutics.
search_peptide_stability_issues	Peptide stability/half-life failures.
search_failed_protacs	PROTACs that failed degradation/ternary/permeability.
search_protac_e3_issues	PROTAC E3-ligase recruitment / ternary failures.
search_failed_oligonucleotides	ASOs/siRNAs that failed engagement/developability.
search_oligo_delivery_failures	Oligonucleotide delivery failures.
search_failed_vaccines	Failed/terminated vaccines (by pathogen/indication).
search_vaccine_immunogenicity_failures	Failed vaccine immunogen designs.
search_failed_adcs	ADCs that failed at any stage.
search_adc_linker_failures	ADC failures attributed to linker chemistry.
search_failed_bispecifics	Bispecifics that failed at any stage.
search_bispecific_format_failures	Bispecific format/engineering failures.
search_admet_failures_all_modalities	ADMET failures across ALL modalities.
search_drug_drug_interaction_failures	Drug-drug interaction failures.
search_mechanism_failures	Approaches that failed for a mechanism (by target).
search_failed_replications	Findings that failed to replicate.
search_safety_failures	Clinical/preclinical safety failures across modalities.
search_target_history	ALL failed approaches against a target across every modality.
search_indication_history	ALL failed approaches for an indication across every modality.
search_pathogen_history	Vaccine + antimicrobial + antibody failures for a pathogen.
get_compound	A compound + its full negative profile across modalities/sources.
get_finding_provenance	Full provenance + detail for a single finding by id.
get_target_landscape	Target "graveyard" / exhaustion index — how picked-over a target is, by modality and outcome.
list_top_targets	The most heavily-pursued targets, ranked by recorded negative findings.
list_models	Summary of the Layer-1 inactivity-scoring model registry.
get_model_card	Per-target Layer-1 model card: training counts + held-out scaffold-split metrics.
get_coverage	Per-modality and per-source coverage stats.

Links

• Website: https://nullary.ai
• Docs: https://nullary.ai/docs
• Coverage: https://nullary.ai/coverage
• Research: https://nullary.ai/research
• MCP Registry: listed as ai.nullary/nullary
• Smithery: https://smithery.ai/badge/nullary/drug-discovery

License

This documentation repository is MIT-licensed. The underlying data is provided under each source's respective license — see the coverage page.