Nowadays, with a growing number of produced nanoparticles, the question related to human and environmental safety arises. Because of their small dimensions, nanoparticles may overcome biological membranes more easily. The detailed pathway is still not understood well and, therefore, toxic potential of many nanoparticles remains unclear. Although several experimental techniques are able to capture changes in biomembranes, many effects may be effectively studied only using computational modeling. Therefore, in the first part of this article, basic experimental and simulation methods often used in the study of nanoparticle-biomembrane interaction will be shortly introduced, and, in the following part, the most recent relevant modeling studies published since 2008 will be reviewed with an emphasis on key factors playing role in nanoparticle-biomembrane interaction.