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