Symmetric formimidoester disulfides (DSs) have recently been identified as a new class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. Given that three geometric isomers for DSs are possible, a computational strategy based on molecular docking studies, followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was used in order to identify the most probable DS isomer interacting with RT, to elucidate the atomic details of the RT/DS interaction, and to identify key features impacting DS antiretroviral activity. The CoMFA model was found to be the more predictive, with values of r(2)ncv, r(2)cv, SEE = 0.264, F = 80, and r(2)pred=0.73.