The bioactive mechanism, by which living tissues attach to and integrate with an artificial implant through stable chemical bonds, is at the core of many current medical applications of biomaterials, as well as of novel promising applications in tissue engineering. Having been employed in these applications for almost 40 years, soda-lime phosphosilicate glasses such as 45S5 represent today the paradigm of bioactive materials. Despite their strategical importance in the field, the relationship between the structure and the activity of a glass composition in a biological environment has not been studied in detail. This fundamental gap negatively affects further progress, for instance, to improve the chemical durability and tailor the biodegradability of these materials for specific applications. This paper reviews recent advances in computer modelling of bioactive glasses based on molecular dynamics simulations, which are starting to unveil key structural features of these materials, thus contributing to improve our fundamental understanding of how bioactive materials work.