Currently Available Scaffolds and MMP Cores in ChEMBL 20

A collection of molecular scaffolds and Matched Molecular Pair (MMP) cores derived from high-confidence bioactive compounds in the ChEMBL 20 database. It includes 35,872 target-based BM scaffolds for Ki and 74,379 for IC50, among other counts for CSKs and MMP cores. The dataset was compiled by Ye Hu at the University of Bonn.

Use Cases

• Analyze scaffold diversity in bioactive chemical space based on the provided scaffold counts.
• Train models for molecular property prediction based on scaffold and MMP core features.
• Design focused compound libraries for specific target classes based on the extracted BM scaffolds.
• Study structure-activity relationships (SAR) using the retrosynthetic MMP cores.

Strengths

• Derived from ChEMBL version 20, a well-known and trusted source for bioactive molecule data.
• Provides specific counts for different scaffold and core types (e.g., 35,872 BM scaffolds for Ki).
• Focuses on high-confidence bioactive compounds, which likely improves data reliability for modeling.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale modeling tasks.
• Last update date is unknown; freshness unverified.

Provenance

Source

ChEMBL version 20 database.

Collection Method

Extracted from high confident bioactive compounds in ChEMBL.