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negative-results-mcp

negative-results-mcp

by nullary-ai
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Remote

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.

Related MCP server: BioBTree

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

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 deployed

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Maintenance

ActivityInactive
ResponsivenessNo recent community issues

Resources

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