3DID - download page

Flat data files

The flat files downloadable here contain the core information of 3did: interacting 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 details: 3did_flat.gz, 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.

3did_flat

#=ID	the two interacting domains, plus their Pfam IDs
#=3D	one structural instance of this interaction, with the following fields: PDB chain1:(domain1Start-domain1End) chain1:(domain1Start-domain1End) score Zscore

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.

3did_dmi_flat

#=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 motifChain:motifStart-motifEnd motif_sequence number_of_contextual_contacts interaction_topology_(with respect to the domain)

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.

3did_interface_flat

#=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 in the Pfam HMM profile of the currently used version.

3did_global_interface_flat

#=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. If you would like a version of the 3did_global_interface_flat file that also contains interfaces with just a single partner, contact us.

MySQL tables

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

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 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.

Questions?

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, D413-D417.

Should you have any questions, contact us at 3did(at)irbbarcelona.org.