I would like to identify structural homologs in the PDB for a protein without any regard to sequence identify. Is there a way to do this with Schrödinger software?

Yes, this is supported from Suite 2008 on. It unfortunately does not work in Suite 2011, but it was fixed in Suite 2012.

Instructions for running a structural search against the PDB:

1. Download the following database file, which contains a snapshot of non-redundant structures from the PDB generated on 8 Apr 2012:
   
   https://docs.google.com/open?id=0B-qRWhJqQzmbQjB5Q3ctWFp1Z1U
2. Create an input file (jobname.inp, e.g. search.inp) containing the following three lines:
   
   MODE scan
QUERY_FILE query-PDB-file
DATABASE path/skandb-Apr2012.gz
   
   Note that the name of the query PDB file cannot contain path information.
   
   If your template protein only has two secondary structure elements (e.g., helix-turn-helix), add the following line to the input file:
   
   SSE_MINLEN 2
   
3. Run SKA:
   
   $SCHRODINGER/ska jobname
   
   for example:
   
   $SCHRODINGER/ska search

The output from the structural search will be in jobname.out (e.g. search.out)
   
4. View the output using the SKA Results Viewer:
   
   $SCHRODINGER/utilities/SkaResultsViewer output-file


Keywords: Structural homolog, PDB, align

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