SiteHopper 1.0.0

July 2021

This is first release of the SiteHopper application suite. SiteHopper can search a database containing hundreds of thousands of design units for proteins with similar binding sites to a query design unit in a few minutes using an NVIDIA GPU. SiteHopper can also create this database from a series of biomolecular structures in OEDU format. The SiteHopper application suite consists of the following applications:

• sitehopper_build generates a database of patches from design units to be searched with sitehopper_search.

• sitehopper_search searches a database of design units for proteins with binding sites similar to a query design unit.

• A large database of patches based on the public is available for download in a platform-independent format.