DoGSite3

Overview

DoGSite3 was developed for predicting robust and reliable small molecule binding sites and computing their geometrical and chemical descriptors. It is based on the grid-based DoGSite algorithm for predicting pockets and their sub-pockets. The new tool is largely rotation- and translation-invariant due to a normalization procedure before binding site prediction. Known ligands in the structure can be used to bias the grid by sufficiently buried ligand fragments. The output encompasses novel chemical binding site descriptors considering solvent accessibility. Compared to its predecessor, it shows increased robustness through comprehensive parameter optimization. DoGSite3 runs finish within seconds.

Limitations

Currently, DoGSite3 does not report a measure of binding site druggability.

Software Availability

DoGSite3 is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download DoGSite3, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run DoGSite3. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Graef, J.; Ehrt, C.; Rarey, M. Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. J Chem Inf Model 2023, 63 (10), 3128-3137. DOI: https://doi.org/10.1021/acs.jcim.3c00336