ECOD classification of the Salmonella enterica pangenome (AlphaFold models)

ECOD (Evolutionary Classification of protein Domains) classifications for representative proteins of the Salmonella enterica pangenome (79,758 genomes), from AlphaFold models partitioned and classified with DPAM, with flags for proteins over-represented in clinical isolates (potentially pathogenic). This is the data set behind Medvedev et al. (2024) Sci Rep 14:12260 (doi:10.1038/s41598-024-60991-x).

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

Contents: 17,234 classified domains from 10,361 representative proteins; 3,760 domains on 2,430 potentially pathogenic proteins.

• ecod_salty.domains.tsv: one row per domain, with NCBI and UniProt accessions, residue range, pathogenicity flag and full ECOD lineage (main table)
• ecod_salty.models_ncbi.pdb.tar.zst: the 10,361 full-length AlphaFold models the domains were cut from, one per NCBI protein (domain ranges refer to these)
• ecod_salty.models.tsv: per-model provenance (UniProt accession, length, AFDB header, pLDDT range)
• salty_dpam_domains.ncbi.txt: the DPAM domain list with probabilities and unmerged ranges
• ecod_salty.tables.tar.zst and ecod_salty.pgdump: the full PostgreSQL database, as per-table TSV and as a pg_dump

See README.md for column definitions and provenance.