In Advanced Search, DOMMINO provides 4 types of search terms: Interaction type, SCOP Family, Organism, and Keywords; the User can add up to 5 terms for one query. The advanced search will return the list of qualifying PDB records with the following information provide for each PDB structure (i) organism information, (ii) number of interfaces in the PDB structure, and (iii) interaction types with the number of interactions for each type.
Interaction term:
Interaction types are defined by interactions between protein subunits that belong to six pre-defined subunit types: Domain (D), C-Terminal (C), N-Terminal (N), Peptide (P), Interdomain Linker (L), and Undefined chain (U). The interaction type is represented in the form 'Subunit-Subunit (N)' where Subunit is one of the six subunit types and N is the number of interactions of the interaction type in the selected PDB structure For example: D-P stands for the interaction type of between Domain and Peptide subunits.
SCOP Family term:
SCOP Family term used in the DOMMINO query is the SCOP Family SUN ID (see http://scop.mrc-lmb.cam.ac.uk/scop/). It should be a unique numeric ID defined by the SCOP database. For example: SCOP ID 55551 correspond to the 'SH2 domain' SCOP Family.
Organism term:
Organism term can be either a scientific name (e.g., Homo Sapiens) or a common name (e.g., human) of the organism.
Keyword term:
Keyword term can be any keywords related to the description of the complex. For example: SH3 domain.
