Starting from a neutralizing antibody–bound G protein complex (PDB 8JA5), I identified five sets of residues forming contacts with the G protein across five distinct loops. Keeping these interacting residues fixed, I used RFdiffusion to generate binders that preserve these contacts. Binder sequences were then designed with ProteinMPNN and folded with AlphaFold3. I filtered candidates using pLDDT, iPTM, global RMSD, and designed-interface RMSD to select stable, high-confidence designs.
id: strong-gecko-ember

Nipah Virus Glycoprotein G
0.79
--
--
--
52
id: bright-quail-ruby

Nipah Virus Glycoprotein G
0.62
62.78
--
8.0 kDa
69
id: noble-panda-opal

Nipah Virus Glycoprotein G
0.38
73.80
--
7.5 kDa
61
id: amber-kiwi-opal

Nipah Virus Glycoprotein G
0.29
--
--
--
94
id: quick-lynx-maple

Nipah Virus Glycoprotein G
0.29
--
--
--
69
id: violet-yak-leaf

Nipah Virus Glycoprotein G
0.25
69.14
--
5.5 kDa
45
id: hollow-panther-plume

Nipah Virus Glycoprotein G
0.24
78.38
--
7.5 kDa
64
id: calm-crow-stone

Nipah Virus Glycoprotein G
0.17
--
--
--
80
id: silent-otter-ruby

Nipah Virus Glycoprotein G
0.09
--
--
--
53
id: silent-crane-wave

Nipah Virus Glycoprotein G
0.01
83.96
--
8.8 kDa
73