DNA footprinting is a collection of experimental methods used to describe the sequence specificity of DNA-binding proteins. 3D-footprint is a database that employs a computational approach in order to analyse sequence recognition in protein-DNA complexes of known structure, reporting those molecular contacts that contribute most to recognition. The pipeline followed to produce each entry in the database can be summarized as a flowchart. The database contains a selection of 95% non-redundant monomeric complexes updated weekly, plus a complementary collection of redundant and multimeric complexes. Entries are named by concatenating the Protein Data Bank (PDB) structure identifier and the protein chains that take part in the complex. For instance, 1cgp_AB, is a dimeric complex made by protein chains A and B of PDB entry 1cgp. The report for each entry might include:

sitesourcecurationmatches (E-value)
TAATCCPubMed2hdd_A(1.19e-06), 2hdd_AB(9.77e-06)
TAATTAPubMed2hdd_A(1.37e-03), 1hdd_CD(1.65e-04), 3hdd_AB(4.91e-08)
TTAATTPubMed2hdd_A(1.37e-03), 3hdd_AB(1.09e-04)