New Paper: Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3

5 May 2023

Photo: Joel Graef

Detecting binding sites in protein and nucleic acid structures is a crucial starting point for structure-based investigations for enzyme function predictions, virtual screening, and other applications in rational drug design. DoGSite3 now enables a highly robust and reliable detection of small molecule binding sites. It is a grid-based method using a Difference of Gaussian filter to detect pockets in 3D macromolecular structures. It is a reimplementation of the well-known DoGSite algorithm with optimized parameters and an option to bias detected pockets with respect to bound ligands. Global properties, describing the size, shape, and chemical features of the predicted (sub-)pockets are calculated. Check out this recent publication for details regarding method improvements, parameter optimization, and binding site detection performance: https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c00336. You can test DoGSite3 for your protein of interest on ProteinsPlus at https//proteins.plus. If you want to process larger datasets of macromolecular structures, you can also download the tool as part of the NAOMI ChemBio software collection at https://uhh.de/naomi.