To design a motif-preserving binder against the Nipah virus, the pipeline begins by identifying the m102.4 interface residues that contact the viral epitope specifically mapping the interaction onto the region (hotspot) of Nipah G as represented in structure 2VSM, chain A - which defines the motif that must remain unchanged. RFDiffusion is then used to generate new backbones that correctly position this fixed motif relative to the corresponding 2VSM chain-A hotspots, creating diverse but geometrically compatible scaffolds. ProteinMPNN subsequently designs sequences for the newly generated backbones while keeping all motif residues fixed, and ProtRL refines these sequences to improve foldability and interface plausibility. The designs are evaluated with structure prediction and filtered by pLDDT to ensure conformational reliability, and the surviving candidates undergo Boltz2 and minimal iPSAE scoring to prioritize those with the most favorable energetic and interface-packing characteristics, yielding a curated set of high-quality, motif-preserving binders.
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