The correlation between score and pKi are different for the protein targets in question. For example, nuclear hormone receptors ER and AR have positive correlation values instead of the expected negative ones. In addition, the best selector/ranker pair for HIV proteases in the PDBbind core set is RMC15/RMR6 which is the opposite pair for all proteins in general. Therefore, the use of different scoring function may be advantageous in ranking the relative binding affinity of given ligands to the protein targets in a particular class of proteins.