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

License

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

This server cannot be installed

A

license - permissive license

-

quality - not tested

C

maintenance

How are these scores calculated?

Resources

GitHub Repository

Need Help?

Related Servers

Unclaimed servers have limited discoverability.

Looking for Admin?

If you are the server author, to access and configure the admin panel.

negative-results-mcp