Use a de-novo binder design scheme to target a surface of Nipah Glycoprotein G that binds single domain antibody n425 (PDB: 8XPY).

The de-novo design protocol uses a sequential optimization approach with decisions trees to explore parameters space. The design loop leverages RFdiffusion, different flavors of ProteinMPNN, and AlphaFold2. The two (predicted) best scaffolds from this design are included here (2445 and 2447), then additional variants were generated using the same scaffold of 2445 and 2447 using ProteinMPNN (these variants were scored and selected using Boltz2 without templates). No selection on the basis of IPSAE has been performed here.

Only the best design is submitted here.