Safety Filter Scoring

Safety filter scoring evaluates molecules against structural alert databases to identify potentially problematic compounds. This is a scored summary of the detailed Structural Alerts screening.

What It Measures

Safety filter scoring tests molecules against multiple catalogs:

Catalog	Patterns	Focus
PAINS A/B/C	~480	Pan-assay interference compounds — frequent hitters in HTS
Brenk	~105	Unfavorable chemical moieties for drug development
NIH	~180	NIH MLSMR screening exclusion filters
ZINC	~95	Drug-likeness and reactivity filters
ChEMBL	~700+	Combined from 7 pharma sub-catalogs (see below)

ChEMBL Sub-Catalogs

The ChEMBL structural alerts combine filters from 7 pharmaceutical industry sources:

Sub-Catalog	Source	Focus
BMS	Bristol-Myers Squibb	Reactive functional groups and chemical liabilities
Dundee	University of Dundee	Promiscuous compound filters for screening
Glaxo	GlaxoSmithKline	Undesirable moieties and toxicophores
Inpharmatica	Inpharmatica Ltd.	Chemical liabilities and ADMET flags
LINT	Lead Identification Noise	Noise-causing patterns in lead identification
MLSMR	NIH/MLSMR	Molecular Libraries Screening Center Network filters
SureChEMBL	EMBL-EBI	Patent literature structural alerts

Each sub-catalog targets different aspects of compound quality. When ChEMBL alerts are enabled, all 7 sub-catalogs are screened simultaneously.

All pattern matching uses RDKit's FilterCatalog module with SMARTS substructure matching.

Scoring Output

The safety filter score provides a pass/fail summary:

{
  "safety_filters": {
    "pains": {
      "passed": true,
      "alerts": [],
      "alert_count": 0
    },
    "brenk": {
      "passed": true,
      "alerts": [],
      "alert_count": 0
    },
    "nih": {
      "passed": true,
      "alerts": [],
      "alert_count": 0
    },
    "zinc": {
      "passed": true,
      "alerts": [],
      "alert_count": 0
    },
    "chembl": {
      "passed": true,
      "total_alerts": 0
    },
    "all_passed": true,
    "total_alerts": 0,
    "interpretation": "No safety alerts detected"
  }
}

Interpretation

Result	Interpretation	Recommendation
All passed	No alerts found	Good safety profile for screening
PAINS only	Assay interference risk	Review assay compatibility before screening
Multiple catalogs	Multiple issues	Investigate further, consider excluding

Safety Filter vs. Structural Alerts

Safety Filter Scoring (this page):

• Part of comprehensive scoring API
• Pass/fail summary only
• Quick screening
• Included in batch processing

Structural Alerts:

• Detailed alert information
• Matched atoms identified
• Pattern names and descriptions
• Dedicated API endpoint

Use safety filter scoring for quick filtering, then use detailed structural alerts for investigation.

Use in Batch Processing

In batch mode, safety filter pass rate is reported:

{
  "statistics": {
    "safety_pass_rate": 0.91
  }
}

This indicates 91% of molecules pass all safety filters.

Best Practices

1. Use for prioritization: Not absolute rejection criteria
2. Review alerts: Always investigate specific alerts for hits
3. Consider context: 87 FDA-approved drugs match PAINS patterns
4. Check assay type: PAINS alerts are assay-specific
5. Document decisions: Record why you accepted/rejected flagged molecules

Next Steps

• Structural Alerts - Detailed alert information
• Scoring Overview - All scoring systems
• API Reference - Full API documentation