How to query SCORPIO

Protein

The protein can be selected by name, classification, source and E.C. number. The protein names, classifications and sources are available as drop down menus. The E.C. number can be typed into the box. If a partial E.C. number is entered all the members of that class will be returned, i.e. "3." will return all the hydrolases.

The search fields are additive so the combination protein name "HIV-1 Protease" and classificaton "Ligase" will not return any results as HIV-1 protease isn't a ligase.

If you want to select all the proteins in the database leave the drop down menus as "Any..." and leave the E.C. number field blank.

Ligand

The ligand can be selected by name and class, which are both available as drop down menus. The classes currently available to filter the ligands are "Carbohydrate", "Lipid", "Peptide" and "Miscellanous", where the latter holds all the entries that don't fit into any other class.

The protein and ligand selections are addative so as to be able to filter down the number of hits.

By selecting a paricular ligand or ligand class and leaving all the protein settings as "Any..." you can retrieve all the proteins that interact with your particular ligand of interest.

Search

Five search options are available. The "All Info" option returns all the information available for your protein/ligand/protein-ligand query. The "Holo structures with ITC data" option only returns the hits that have both structural and ITC data for your paricular query. The "ITC data" option returns all the hits where ITC data is available. Similarly the "Holo structures" and "Apo structures" options return all the hits where a holo/apo structure is available.

In order to get any returns from the "Apo structures" option some sort of protein selection must be made.