Fig. 1

Structure-based correlation network of the mutant protease-PI complexes. a Thirty-three protease-PI mutant complexes (represented by nodes) are coloured according to seven PIs: Atazanavir (ATV, cyan), Darunavir (DRV, blue), Indinavir (IDV, red), Lopinavir (LPV, yellow), Nefinavir (NFV, magenta), Saquinavir (SQV, green), and Tipranavir (TPV, purple). The protease-PI complexes are numbered following indices: 0 (the PDB available complex structure that was used to initiate the reported mutations), 1 (mutated protease-PI complexes containing both major and minor mutations), the rest from 2 to 6 (mutated protease-PI complexes containing minor mutations). In this network, edges are coloured based on the source node, which are connected to other nodes; hence highlighting the link from one node to the others. The node sizes are varied based on different related closeness level of each node to other nodes. b A consolidated graph that shows predominant trends that the protease is most likely to resist, from one PI to another. The thicker the arrows are, the more likelihood that protease mutations extend the resistance to the corresponding PIs. The graph was generated using Gephi v0.82 [37]