SiteHopper_search is used to search a database of proteins for binding sites similar to a query protein.
An NVIDIA GPU is required to run SiteHopper_search.
Output from SiteHopper_search¶
SiteHopper_search will two files: a log file and an oedu file. The log file contains scores from the top hits, as well as any warnings or errors encountered. The oedu file holds the design units for the hits, as well as a surface representation of the binding site. The design units contains the hit protein, the bound ligand if there was one, solvent, excipients, and other cofactors. The proteins are tagged with Patch Score, Patch Shape Score, and Patch Color Score. These values can be found in the spreadsheet window in VIDA.
Scoring in SiteHopper_search¶
SiteHopper_search orders hits according Patch Score. Patch Score is a modified version of Tanimoto scoring from shapetk. Instead of calculating a color tanimoto from 0-1, SiteHopper_search calculates a color tanimoto from 0-3. This value is called Patch Color Score. The shape tanimoto is calculated the same as in shapetk, and called Patch Shape Score. The resulting Patch Score in SiteHopper_search is equal to the sum of the Patch Color and Patch Shape scores, analogous to how the tanimoto combo score is the sum of tanimoto shape and color. Patch Score ranges from 0-4, rather than 0-2, with 4.0 being perfect overlap, and 0.0 being no overlap. The shape and color components are output alongside the combo score in the log file, and can also be viewed in the spreadsheet window under the protein tab in VIDA.
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:
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.