Published February 18, 2025 | Version v1
Dataset Open

ISS Databases

Authors/Creators

Description

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

Files

Files (20.4 GB)

Name Size
md5:47786a14ceda037a9b75499de5f4f73d
23.3 MB Download
md5:a77534fa5428ffabce7ca95675c07681
15.6 MB Download
md5:0a81d86b4dae786f8bc0f428cfb0b3ce
43.6 MB Download
md5:cd1c646c605c7fe95f9c6585fc5a6ad6
20.0 GB Download
md5:503cfd39ff7b31763849e54347faf5af
225.5 MB Download
md5:efabe7247c19bb0ed8c46e83c2b48ae3
12.0 MB Download