The design pipeline started from a known high-affinity binding protein as a template. The T4 phage tag (T4-tag) was genetically fused to its terminus with a flexible linker. The tertiary structure of the fusion protein was then predicted using AlphaFold3 to assess the feasibility of the design. The predicted model was rigorously analyzed in Discovery Studio, where it was superimposed onto the original template to ensure the structural integrity of the binding scaffold was maintained (low Cα RMSD). The final selection was based on the optimal conformation where the T4-tag was properly exposed without perturbing the native fold of the parent protein.
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