3DID - download page
Flat data files
The flat files downloadable here contain the core information of 3did:
domain pairs (ID) and instances of this interaction in structure along with InterPreTS
scores (3D; P. Aloy and R.B. Russell, 2003, Bioinformatics), and contact
domain-motif interactions (motifs with pattern and source database as well as
all 3D instances of the interaction type): 3did_dmi_flat.gz, and interface
flat files for the different binding topologies (the interface numbring refers to the domain's Pfam HMM profiles): 3did_interface_flat.gz as
well as global interface flat files (where the numbering again refers to the
Pfam HMM profiles, and the (fraction) indicates how many of the binding
partners use this residue 3did_global_interface_flat.gz.
Here's a brief description of the flat file format. If you need more
information, please send us an email.
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 are in PDB seqRes numbering.
Two slashes (//) indicate the end of a domain pair.
|#=ID|| the two interacting domains, plus their Pfam
|#=3D|| one structural instance of this interaction, with the
following fields: PDB chain1:(domain1Start-domain1End)
chain1:(domain1Start-domain1End) score Zscore|
For each interaction between this pair of domain and motif, a #=3D entry is
given, again using PDB seqRes numbering. // indicates the end of a pair.
|#=ID|| domain (source database - currently Pfam only) motif (source database, if any)|
|#=PT|| the motif pattern, and the date when it was retrieved, if applicable|
|#=3D || PDB domainChain:domainStart-domainEnd
interaction_topology_(with respect to the domain)|
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 in the Pfam HMM profile of the currently used version.
|#=ID|| <domain1> <domain2>|
|#=IF|| <topology ID>: <contacting regions>|
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. If you would like a version of the
3did_global_interface_flat file that also contains interfaces with just a
single partner, contact us.
|#=ID|| <domain1> <domain2>|
|#=BD|| <binding partner (domain or peptide)>
(<topology ID>), [DDI|DMI]|
|#=PS|| <HMM profile position> (<fraction of binding partners using
The MySQL tables contain all the information available online (3did.sql.gz).
- Residue numbers in the PPI and residue tables refer to the PDB residue
- Due to MySQL's case insensitivity, lowercase chains are stored as "xx"
instead of "x".
- As described above, 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.
For more detailed descriptions please refer to our publications:
Amelie Stein, Arnaud Ceol & Patrick Aloy.
3did: identification and classification of domain-based interactions of known three-dimensional structure
Nucleic Acids Res. 2011, 39, D718-723.
A. Stein, A. Panjkovich & P. Aloy: 3did Update: domain-domain and peptide-mediated interactions of known 3D structure
Nucleic Acids Res. 2009, 37, D300-304.
A. Stein, R.B. Russell & P. Aloy: 3did: interacting protein domains of known
three-dimensional structure. Nucleic Acids Res. 2005, 33,
Should you have any questions, contact us at 3did(at)irbbarcelona.org.