The SiteHopper TK uses technology from the OpenEye Shape TK to compare protein binding sites using Shape and Color similarity.
There are two main classes in the toolkit. OESiteHopperDatabase can be used to search and prepare a set of OEDesignUnit for search. For each OEDesignUnit, OESiteHopperDatabase creates a “patch” molecule generated by placing shape atoms on the molecular surface of the binding site and color atoms on protein atoms near the binding site.
Once the database is created, the OESiteHopperSearch class can take a query OEDesignUnit and return a set of similar OEDesignUnit objects, each transformed based on the optimized overlap and scored using a combination of the Shape and Color Tanimoto calculated via the Shape TK.
If running on a Linux machine with a supported Nvidia GPU, the Search can use the GPU to do a fast pre-screen to speed up the search. See the GPU Prerequisites section for more info on GPU requirements.