Nipah Virus Glycoprotein (PDB 2VSM chain A) was truncated (residues 483-601) to be used as the target for binder design using BoltzGen. The binding regions within the truncated target were defined as 488-505 ; 527-534 ; 553-557 ; 582-586 (ie loops that interact with Ephrin-B2). 20000 binders (random size between 80 and 140 residues) were generated by BoltzGen in 4 steps: Design – Inverse Folding – Refolding – Design Refolding. Data analysis and filtering for the top 60 binders were performed using default values. The 60 sequences were then re-analyzed by LocalColabFold running AF2 multimer and Boltz-2 using the full length sequence of the Nipah Virus Glycoprotein extracellular domain (188-602). The 60 protein/binder complexes were ranked by decreasing values of ipSAE max and binders with ipSAE > 0.7 were submitted.
id: azure-panda-cloud

Nipah Virus Glycoprotein G
0.69
90.19
--
9.0 kDa
83
id: violet-dove-frost

Nipah Virus Glycoprotein G
0.59
78.11
--
10.1 kDa
103
id: silver-ox-thorn

Nipah Virus Glycoprotein G
0.53
87.84
--
10.3 kDa
88
id: quiet-gecko-ember

Nipah Virus Glycoprotein G
0.01
53.13
--
9.0 kDa
92