Supplement for AutoPSI DB

Individual SCOP classification predictions (UNIX text files, MySQL output):

• UniProt, predicted regions based on InterPro patterns: Complete list (80MB, more than 500MB unzipped)
• PDB, predicted regions based on InterPro patterns: Complete list (3MB, more than 80MB unzipped)
• PDB, predicted regions based on Vorolign: Complete List (3MB, unzipped)

In the entry dialog, you can choose between three different search options: PDB ID, UniProt ID and Description. The first two of these will search against the respective databases using the LIKE mechanism of MySQL, i.e. they will match every ID where the searchterm is a substring. The description search does the same for all one-line descriptions in both PDB and UniProt.

Behind the search field, you can see the expected number of results. This will show you how many results match your current searchterm. However, for both memory and speed issues, we decided to limit our results table to a maximum of 500 hits per database (i.e. PDB or UniProt). Therefore, if your searchterm matches more entries than 500 per database, not all will be shown.

Once you have done the search, the result list will show you the matched items. Clicking on an item will open a new tab with detailed information on it, the "detail view".

In the detail view, you will find three group boxes. The first contains a structure visualisation, if a structure is available. This is a JMOL plugin, i.e. you can use all JMOL feature in this window, even the console, for coloring and selecting residues you are interested in The second box contains a schematic view of the regions on a protein chain for which we have annotated domains or predicted SCOP classifications. Clicking on the boxes for PDP, SCOP, Vorolign or Patterns will highlight the corresponding region in the structure, if available. The third box contains a tabbox with detailed information on the protein, the domains and the found predictions. Clicking on the list boxes for Vorolign and Patterns will open a popup window with links to external databases.

AutoPSI DB uses AutoSCOP annotated InterPro patterns, Vorolign predictions and the consensus of both. The individual methods as servers can be found here:

• AutoSCOP (Pattern-based SCOP classification prediction)
• Vorolign (Structural alignment server)