Examining the failures of a method to produce the desired outcome can illuminate potential issues with the algorithm and can be used to address these problematic areas in the future. In the case of CANDOCK, only 12 out of the 285 protein complexes in PDBbind proved to be complete failures, that is, no combination of method and 'Top Percent' could yield a predicted pose within 2.0 Å of the crystal pose. Of these 12, six complexes (1H22, 1H23, 3AG9, 3KWA, 3UEU, and 4EA2) contain an aliphatic carbon chain greater than 4 atoms. This is significant as the fragmentation of ligands does not consider aliphatic chains to be fragmented and uses a separate strategy for determining the location of linkers in these molecules and therefore have a high ratio of rotatable bonds to ligand fragments. Also, aliphatic chains consist of the same atom type (sp3 hybridized carbon; C3) repeated in 3D space. We plan on addressing this issue in later versions of CANDOCK by using a different sampling method and ligandclass specific scoring function, similar to what was done for the support of carbohydrates in Autodock Vina 38 .