A curated multi-endpoint drug-protein bioactivity dataset with construct-aware protein targets
TL;DR
Crate-DTI, a construct-aware dataset derived from the 1 July 2026 BindingDB export, with IC50, Ki, Kd and EC50 processed independently, supports endpoint-specific classification and regression while allowing users to select molecular representations, protein representations and evaluation splits.
Abstract
Public drug-protein bioactivity resources commonly identify targets by UniProt accession, although one accession may represent distinct experimental sequences. We present Curate-DTI, a construct-aware dataset derived from the 1 July 2026 BindingDB export, with IC50, Ki, Kd and EC50 processed independently. The release contains 2,919,717 measurements, 1,291,872 standardized ligands, 9,668 sequence-defined protein entities and 2,275,683 endpoint-specific interactions spanning 8,336 reviewed UniProt accessions. Protein entities combine the accession with the reported experimental sequence, preserving constructs that accession-only processing would merge. Across the four endpoints, 4,204 endpoint-specific ligand-accession groups showed different classification labels across sequence-defined protein entities. Exact and inequality-qualified observations provide relation-aware classification evidence, whereas regression targets use exact values only. Connected Parquet tables preserve individual measurements, standardized structures, protein sequences, aggregated interactions and available assay and source provenance. The resource supports endpoint-specific classification and regression while allowing users to select molecular representations, protein representations and evaluation splits. Preprocessing code, a column dictionary, exclusion reports and validation summaries accompany the release.
