Example CommandsΒΆ

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 proteins output, 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.