Protein Operating System (ProOS - Prose) is a muti toool integration pipeline using most of the SOTA tools. It ingests reference structures, maps epitope hotspots, prepares the structure for tool compatability. Generation of novel designs or backbones uses BoltzGen, Bindcraft, RFdiffusion, or Proteina Complexa. Protein stability or solubility mutagenesis occurs with ProtienMPNN, Refold and scoring with ESMFold or Boltz2 and scoring filtering. A unique fusion module takes epitope compatible binders and fuses them to create a single chain biparatopic binder to harness avidity to improve affinity. A novel polishing method uses cycles of MPNN mutagenesis combined with Botlz2 refold and scoring to "lead optimize" sequences and explore the adjacent sequence and fitness landscape.