Holo Sites. The initial list of 2,294 PDB coordinate files for high-resolution co-crystal structures of experimental covalent ligand-bound proteins (herein referred to as holo-protein) was scraped from the covPDB database . A summary data file containing residue-and chain-specific annotation information was obtained directly from the covPDB website. Each annotated covalent site was subject to visual inspection (manual) for containment of the covalent ligand in a pocket-like cavity of the residue and saved as refined list (covPDBs, SupplementaryFile1).