Tutorial
Basic Search
This is the basic search function in DOMMINO. By entering one PDB ID and clicking 'Search', it will return the PDB record with organism information, number of interfaces in this PDB entry, and interaction types with the nubmer of interactions of each type.
By clicking the number of interactions, you will be shown the details of interactions and the network for this PDB entry.
Choose an interaction pair and view the interaction complex and interface structure.
Several control panels around the Jmol plugin provide additional options for users to show the structure. Complex and Interface panels let users choose the display styles and show/hide surfaces. The Toggle panel allows users to show either only the complexs (two subunits in two colors) or also showing interfaces (all four colors). The fourth panel provides different display mode for specifi residues.
Advanced Search
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 provided 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. The 'Minimal number of contact pairs' provides an option to set a threshold to filter out interactions that have too few contact pairs.
If the result has less than 50 PDB records, a list similar to the result from basic search will show up.
If the result has more than 50 PDB records, you will be promped with a notice to ask for your next move: refine your search or show all PDB IDs.
If you choose to show all PDB IDs, result PDB entries will be listed completely into several lines.
