ECOD Classification of AFDB 48 Proteomes

Domain partitions and ECOD (Evolutionary Classification of protein Domains) classifications for AlphaFold Database models of 48 whole proteomes (16 model organisms and 32 global-health organisms), made with DPAM2 against ECOD develop285. This is the data set behind Schaeffer et al. (2024) PLoS Comput Biol 20:e1011586 (doi:10.1371/journal.pcbi.1011586).

Version 2.0 keeps the seven files of version 1 (2023) unchanged and adds the database, the full domain table, coordinates and sequences.

It was previously served as a website (prodata.swmed.edu/ecod/index_af2.php), which has been retired; this record is the archival copy of the classification and its database.

Contents: 1,063,667 domains from 491,781 proteins: 746,349 good domains (the set analysed in the paper), 224,396 simple-topology, 66,506 low-confidence and 26,416 partial domains.

• ecod_af2.domains.tsv: one row per domain, with proteome, protein annotation, residue range, category and full ECOD lineage (main table)
• ecod_af2.proteomes.tsv: the 48 proteomes with species, TaxID and UniProt proteome
• af2_all.dpam_v5.domains.pdb.tar.gz and ecod_af2.nongood_domains.pdb.tar.zst: domain coordinates (PDB, pLDDT in the B-factor column)
• ecod_af2.domains.fa.tar.zst: domain sequences
• af2_*.dpam_v5.domains.txt and related files: the domain lists as originally published (2023-2024)
• ecod_af2.tables.tar.zst and ecod_af2.pgdump: the full PostgreSQL database, as per-table TSV and as a pg_dump

See README.md for column definitions, provenance and notes. The domain structures are derived from AlphaFold DB models (CC BY 4.0).