This study aims at gaining insight into molecular mechanisms of action of three drug targets of the life cycle of influenza virus A subtype H5N1, namely Hemagglutinin (H5), Neuraminidase (N1) and M2 ion channel (M2), using molecular mechanics and molecular dynamics techniques. In hemagglutinin, interest is focused on the high pathogenicity of the H5 due to the –RRRKK– insertion. MD simulations carried out for H5 in both high and low pathogenic forms (HPH5 and LPH5), aimed at understanding why HPH5 was experimentally observed to be 5‐fold better cleaved by furin relative to the non‐inserted sequence of LPH5. As the results, the cleavage loop of HPH5 was found to fit well and bind strongly into the catalytic site of human furin, serving as a conformation suitable for the proteolytic reaction. The second target, neuraminidase was studied by two different approaches. Firstly with MD simulations, rotation of the –NHAc and—OCHEt2 side chains of oseltamivir (OTV), leading directly to rearrangement of the catalyt...