Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures, development of toy models and simulations to identify fundamental principles of molecular evolution, and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.