sitehopper_search is used to search a database of OEDesignUnits similar to a query OEDesignUnit.


To use GPU prescreen, an NVIDIA GPU is required to run sitehopper_search. See GPU Prerequisites for details. If not GPU is available, search will revert to CPU only search.

Basic Search Process

Search consists of several phases.

  1. GPU prescreen: (assuming a compatible GPU is available and -use_gpu is true). Data is loaded into memory and then searched, keeping the top 5000 hits to send on to CPU Search.

  2. CPU Search: Use -ncpu CPU threads to search. If GPU prescreen, this searches the 5000 results from step 1, otherwise it will search the entire database.

  3. Hitlist processing: Hits are extracted from the database, transformed into their final orientation and if -normalize_and_rescore is used, that will happen in this step.

  4. Writing results files

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:


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.

Pre-Built 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.