Example Commands

The simplest way to run sitehopper_search is by passing in a query DesignUnit and a database.

prompt> sitehopper_search -query 4I0D_A__DU__1B7_A-504.oedu -db SiteHopper.shdb -out hits.oedu

Here, sitehopper_search will search through SiteHopper.db for protein with similar binding sites to 4I0D_A__DU__1B7_A-504.oedu. sitehopper_search will write out the top 200 most similar proteins in oedu format to hits.oedu.

If you want to control the number of results, you may do so with the -max_hits parameter.

prompt> sitehopper_search -query 4I0D_A__DU__1B7_A-504.oedu -db SiteHopper.shdb -out hits.oedu -max_hits 100

The above command will reduce the number of hits written out from 200 to 100.

Another commonly used option is -normalize_and_rescore.

prompt> sitehopper_search -query 4I0D_A__DU__1B7_A-504.oedu -db SiteHopper.shdb -out hits.oedu -max_hits 100 -normalize_and_rescore true

This will normalize the sitehopper scores of the hits by the difference in the size of the binding sites of the query, in this case 4I0D_A__DU__1B7_A-504.oedu, and the size of the hit binding site.