To assess the capacity of the advanced platform to successfully disqualify false-positive covalent sites and minimize the chance of a false-negatives in spite of increased positive detection rates, we selected a new mock list of false-positive sites using the apo-covPDB dataset. This list comprises of the most the superficial (solvent accessible) residue on the apo-covPDB structure whose identity matches the covalent ligand-bound residue in the CovPDB counterpart (Matching-Negative Residue column in the SupplementaryFile1). For instance, the covPDB structure 6CGE is covalent ligand-bound at HIS221 and the apo-covPDB counterpart of this protein is 1BHS. With reference to HIS221, HIS179 represents the most distant matching residue ID in 1BHS. Since HIS179 remained unliganded in the experimental structure of the covalent ligand-bound structure of the protein, it represents the most reliable matching false-positive site. Although a similar list of matching false positives was created for the covPDBs and made available in SupplementaryFile 1, due to the large number of covPDB matching false positive sites and unfeasibility for visual inspection to confirm correct/incorrect prediction for each site, we sufficed our discussion with apo-covPDB matching false-positives (and Cryptic-PDB false-positives, Figure ) evaluation trials of the two platforms. Any matching false positive not found in the apo-covPDB structure or not be superficially exposed although being most distant from the covalently modified residue was omitted from analysis. The cryptic-PDB false positives list comprises residue sites on the most extreme or superficial areas of the protein structure tested to ensure that false-positive detection rates remain loyal when assessing non-ligandable surface residues (SupplementaryFile1).