The structural data is preprocessed as summarized in Finally, as the current approach focuses on the discovery of reversible inhibitors, covalent ligands were also excluded. These were identified by downloading the PDB file corresponding to the KLIFS structure and checking the CONECT records for any connection between the kinase and the ligand. Note that after personal communication with A. Kooistra, 27 two PDB entries were excluded manually (2clx, 4cfn), since the ligand was found to be not covalently bound; and three PDB entries (4d9t, 4hct, 4kio) were added, because the ligands bind covalently but the CONECT entries were missing (see full list of removed structures with covalent ligands in the SI). The dataset after preprocessing consists of 2,801 kinase-ligand structures. Further filtering steps during the fragmentation procedure as described in "(3)