The formation of a nanostructure by self-assembly of a peptide or protein building block depends on the ability of the building block to spontaneously assemble into an ordered structure. We first describe a protocol of fusing homo-oligomer proteins with a given three-dimensional (3D) structure to create new building blocks. According to this protocol, a single monomer A that self-assembles with identical copies to create an oligomer A(1) is covalently linked, through a short linker L, to another monomer B that self-assembles with identical copies to create the oligomer B(j). The result is a fused monomer A-L-B, which has the ability to self-assemble into a nanostructure (A-L-B)(k). We control the self-assembly process of A-L-B by mapping the fused building block onto a planar sheet and wrapping the sheet around a cylinder with the target's dimensions. Finally, we validate the created nanotubes by an optimization procedure. We provide examples of two nanotubes in atomistic model details. One of these has experimental data. In principal, such a protocol should enable the creation of a wide variety of potentially useful protein-based nanotubes with control over their physical and chemical properties.