We employ BAGEL (https://github.com/softnanolab/bagel, https://www.biorxiv.org/content/10.1101/2025.07.05.663138v2) with a protein language model (ESM-2) and sample binder variants from the receptor bound complex (PDB ID: 2VSM). More specifically, we find binder sequences that lead to a very similar embedding direction in the interface in the target viral protein. We do this by using an EmbeddingsSimilarityEnergy in BAGEL, penalizing deviation of such embeddings compared in the receptor-bound complex, to the complex with our newly perturbed/designed sequence. After generating many variants, we cluster to 10,000 designs with mmseqs2 at 80% sequence similarity. Lastly, we fold these with Boltz-2. We submit by filtering with the number of hydrophobic residues, only taking structures with a mean pLDDT above 70, and the ones with the highest ipSAE.
id: mellow-goat-snow

Nipah Virus Glycoprotein G
0.77
61.93
--
2.2 kDa
18
id: shy-dove-opal

Nipah Virus Glycoprotein G
0.77
56.55
--
4.6 kDa
34
id: brisk-goat-bronze

Nipah Virus Glycoprotein G
0.75
65.68
--
1.1 kDa
10
id: radiant-ram-plume

Nipah Virus Glycoprotein G
0.70
61.04
--
3.1 kDa
25
id: violet-orca-pine

Nipah Virus Glycoprotein G
0.69
55.80
--
2.1 kDa
16