ISS Databases

If you use these data, please cite:Liu H, Laiho A, Törönen P, Holm L. 3-D substructure search by transitive closure in AlphaFold database. Protein Science. 2025;34(6):e70169. https://doi.org/10.1002/pro.70169 Here's a description of the files: afdb2_metadata.tsv: Data parsed from the description line of Uniprot Fasta file. Columns: (1) Dali identifier, (2) Uniprot accession, (3) Uniprot protein identifier, (4) Uniprot's short description of the protein, (5) NCBI taxonomy identifier, (6) Uniprot's gene symbol dbref.tsv: Dali identifier mapped to Uniprot accessions Columns: (1) Dali identifier, (2) length of protein, (3) Uniprot accession, (4) Unidprot protein identifier dssp.tsv: Columns: (1) Dali identifier, (2) sequence of three-state secondary structure assignments mini_afdb_afdb.tsv: All-vs-all comparison of AlphaFold Database v2 (AFDB2) structures generated using Foldseek command: foldseek easy-search pdb-directory afdb2 result.m8 tmp -e 1 --max-seqs 50000 Only pairs with e-value below 0.01 are reported (hence prefix mini_). Columns: (1) Dali identifier of query structure, (2) Dali identifier of database structure (sbjct), (3) start of query alignment, (4) end of query alignment, (5) start of sbjct alignment, (6) end of sbjct alignment, (7) Foldseek's e-value sequ.tsv: Columns: (1) Dali identifier, (2) amino acid sequence species_taxid.tsv: Columns: (1) scientific name, (2) NCBI taxonomy identifier