20 native proteins in the test set are misclassified using Strategy 2.

The number of ligands bound to the protein are listed. The molecules are sorted by the fitness value. 14 of them (marked by “”) have ligand(s) bound to the protein. 4 of them (marked by “”) have contacts due to inter chain interactions. The fitness function definitively failed for only 3 proteins (marked by “”). For the remaining 17 proteins, the contacts between organic compounds and metal ions with the protein and inter chain interactions may provide additional stability beyond the intra-residue interactions captured in the descriptors.