Nucleoside-resistant isolates have been identified in patients receiving antiretroviral nucleoside drugs. The different resistance phenotypes seem to correlate with different sets of mutations in reverse transcriptase (RT), and the effect of individual set of mutations on resistance to a specific NRTI can only be presumed by kinetic studies and building up the enzyme active site by molecular modeling studies. However, the understanding how mutations affect RT structure and function, and the ensuing loss of potent antiviral activities of certain NRTIs have not been demonstrated in conjunction with their binding modes, which would provide invaluable insight into the design of more effective NRTIs active against the mutant RTs. This review discusses our recent efforts to assess the structural adjustment resulting from mutations and the accompanying energetic consequences based on the assumption that mutation may either deform the active site conformation through structural realignment or destabilize inhibitor binding.