To date the effect of variations at the protein level is poorly studied in computational drug discovery research. This is mainly due to experimental difficulties in analyzing data at the protein structural level. We previously proposed a post-hoc analysis approach of molecular dynamics simulations using dynamic residue network analysis to consider the dynamic nature of functional proteins and protein-drug complexes and to probe the impact of mutations and their allosteric effects. This talk focuses on examples including drug resistance in infectious diseases; proposing computational approaches for common ways of dealing with different health problems.