Overview

SiteHopper_search is used to search a database of proteins for binding sites similar to a query protein.

Note

An NVIDIA GPU is required to run SiteHopper_search.

Binding site surface visualization

A surface representation of the binding site is included as part of the output design units. An example is shown below:

../../_images/sitehopper_search_binding_site_viz_1UYG.png

1UYG with binding site surface visualization

The surface represents residues that are close enough to interact with the ligand. The surface is comprised of four colors: white, yellow, red and blue. White corresponds to non-polar residues, yellow to polar residues, red to acidic residues, and blue to basic residues.

SiteHopper Database

Included in the SiteHopper product is a large database which can be searched using SiteHopper_search. This database is available for download in a platform-independent format.