I aim to target the cryptic epitope on the Nipah virus G protein based on the available 8xpy PDB structure. This pocket has been validated as functional within the cell and does not compete directly with Ephrin-B2, thus offering a more specific interaction and potentially more powerful biological activity.

In terms of design, the pockets also contain additional structural components, facilitating the binder design.

The structure predicted by AlphaFold3 does not reveal the cryptic pockets; therefore, the starting structure is based on the 8xpy model, which is then corrected using a PDB fixer program. The binders are designed using BindCraft. Subsequently, the binders are predicted again with Boltz2 and ranked by the Ipsae minimum at a 10 Ångström cutoff. The top 20 are visualized, and the top 10 are selected manually.