We have developed ProBiS Tools, a new in silico web and standalone platform for drug discovery based on structural comparisons of protein binding sites. The tools integrate our developed methods that allow to address various problems in medicinal chemistry and structural biology. The binding site comparison algorithm ProBiS (Protein Binding Sites) enables the recognition of common geometric patterns of similar physicochemical properties on protein surfaces independent of the fold homology of the compared proteins. The comparison of the binding sites enables research within the framework of various research projects, including drug repurposing and polypharmacology as well as the prediction of target proteins for natural substances. The GenProBiS method enables the visualisation and investigation of sequence variants within binding sites and the investigation of their possible effects on ligand binding. An extension of this method, the ProBiS-H2O method, enables the prediction of conserved water sites on protein surfaces. The platform also integrates LiSiCA, BoBER and PROTEUS methods that enable research in medicinal chemistry, such as the identification of novel drugs by ligand-based virtual screening and bioisosteric substitutions and, through integration with our database of binding sites, the prediction of novel target proteins for small molecules with unknown activities.

ProBiS tools for drug discovery

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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