Small photochromic molecules are widespread in nature and serve as switches for a plethora of light-controlled processes. In a typical photoreceptor, the different geometries and polarities of the photochrome isomers are tightly coupled to functionally relevant conformational changes in the proteins. The past decade has seen extensive efforts to mimic nature and create proteins controlled by synthetic photochromes in the laboratory. Here, we discuss the role of molecular modeling to gain a structural understanding of photochromes and to design light-controlled peptides and proteins. We address several fundamental questions: What are the molecular structures of photochromes, particularly for metastable isomers that cannot be addressed experimentally? How are the structures of bistable photoisomers coupled to the conformational states of peptides and proteins? Can we design light-controlled proteins rapidly and reliably? After an introduction to the principles of molecular modeling, we answer these questions by examining systems that range from the size of isolated photochromes, to that of peptides and large cell surface receptors, each from its unique computational perspective.