SiteHopper builds on the industry best-in-class 3D shape and chemical feature ligand comparison application (ROCS®) from OpenEye to the domain of protein comparison. Treating binding sites as constructs with a defined shape and set of chemical features allows for rapid searching of a database of known protein structures. You can generate your own protein database to search, or use OpenEye's ready to use protein-ligand binding sites database for your convenience.
What is available in the prepared SiteHopper database?
Two ready to search SiteHopper patch databases are available; ~40,000 known protein-ligand binding sites, and ~300,000 potential protein binding sites. The datasets were generated using ~40,000 prepared design units from roughly 21,000 PDB files. Additional ~106,000 patches of potential binding sites database generated from AlphaFold2 structures is also available.
Can I run SiteHopper on GPU or Cloud?
You can compare a query protein to a database of hundreds of thousands (or millions) of protein binding sites efficiently, thanks to a multi-threaded searching algorithm (GPU on Linux) or harness the scalability of cloud computing.
How can SiteHopper helps in my early drug discovery?
The speed and flexibility of SiteHopper opens new avenues in drug repurposing, predicting off target effects, and polypharmacology among other uses in drug design projects.
For more detailed information on SiteHopper, check out the link below:
Download SiteHopper Poster