We report the synthesis of four different RGD peptide derivatives which spontaneously self-assemble into nanoscale architectures. Depending on the information programmed into the molecular-scale building blocks by organic synthesis, these compounds assemble into different nanoscale morphologies. This process can be fully understood using multiscale modelling which provides predictive insight into subtle differences, such as whether the compounds form spherical micelles, rod-like cylinders or tubular assemblies, and predicts experimentally observed critical aggregation concentrations (CACs). We then probe the multivalent binding of these assemblies to integrin proteins and demonstrate that the spherical micellar assemblies perform well in our solution-phase integrin binding assay as a consequence of self-assembled multivalency, with the CAC switching-on the binding. Conversely, the cylindrical assemblies do not work in this assay. As such, the nanoscale morphology controls the apparent ability to perform as a self-assembled multivalent ligand array.