Flat data files

The flat files downloadable here contain the core information of 3did:

  • 3did_flat.gz contains interacting domain pairs (ID) and instances of these interactions in PDB structures along with InterPreTS scores (Aloy and Russell, Bioinformatics 2003) and details on the contacts;
  • 3did_dmi_flat.gz contains domain-motif interactions, i.e. motifs with the corresponding pattern and source database as well as all 3D instances of the interaction type;
  • 3did_interface_flat.gz contains the different binding topologies (the interface numbering refers to the domain's Pfam HMM profiles);
  • 3did_global_interface_flat.gz contains the global interfaces (where the numbering again refers to the Pfam HMM profiles), and the fraction indicates how many of the binding partners use this residue.

Here you can find a brief description of the flat files format. If you need more information, please send us an email.

  • #=ID: the two interacting domains, plus their Pfam IDs
  • #=3D: one structural instance of this interaction, with the following fields:

    PDB chain1:(domain1Start-domain1End) chain2:(domain2Start-domain2End) score Zscore topology

Below each #=3D entry, the residue contacts are listed (residue 1 and 2, position 1 and 2, and contact type -- m = main chain, s = side chain). Please note that all positions given here refer to the numbering of residues in the original PDB file. Two slashes (//) indicate the end of a domain pair.

  • #=ID: domain (source database - currently Pfam only) motif (source database - currently PLoS_CB_2010 only)
  • #=PT: the motif pattern, and the date when it was retrieved, if applicable
  • #=3D: PDB domainChain:start-end motifChain:start-end motif_seq num_contextual_contacts topology

For each interaction between this pair of domain and motif, a #=3D entry is given, again using the residue numbering of the PDB file. // indicates the end of a pair.

  • #=ID <domain1> <domain2>
  • #=IF <topology ID>: <contacting regions>

There is one #=IF line for each topology determined for this pair of domain and (domain|motif). The contacting residues have been mapped to the corresponding positions in the Pfam HMM profile of the currently used version.

  • #=ID <domain1> <domain2>
  • #=BD <binding partner (domain or peptide)> (<topology ID>), [DDI|DMI]
  • #=PS <HMM profile position> (<fraction of binding partners using it>)

Please note that global interface data is only provided for those cases that involve more than one binding partner. If just one binding partner is involved in a particular interface, the <HMM profile positions> are the same as in the respective 3did_interface_flat entry, and the <fraction of binding partners using it> is always 1.

MySQL tables

The MySQL tables contain all the information available online ( 3did.sql.gz). Please notice that:

  • Residue numbers in the PPI and residue tables refer to the PDB residue numbering.
  • Due to MySQL's case insensitivity, lowercase chains are stored as "xx" instead of "x".
  • As described in the previous section (3did_global_interface_flat), global interface data is only provided for those interfaces that involve more than one binding partner, as the relevant positions for single-partner interfaces are the same as in the interfaces table, and the corresponding fraction of binding partners is 1.
Previous versions

Here you can find the previous versions flat files containing the core information of 3did: