Since the objective of the competition is to disrupt the native interaction between EphrinB2 and the Nipah Virus glycoprotein, we reasoned using the existing binding interface as our starting point may both be more computational efficient and epitope specific. As such, we used Boltzgen to generate 30000 candidate binder sequences, where the interfacial sequences "KENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKN" are kept fixed, and the N-terminus was allowed to diffuse between 60-70 residues, and C-terminus was allowed to diffuse between 30-50 residues to keep the overall length of the de novo binders similar to that of EphrinB2. After the binders have been generated, we applied the default Boltzgen filters to narrow down the candidates, and sorted the filter passing binders by "interaction_pae" and selected all binders meeting with interaction_pae < 12 for secondary screening. These binders are then refolded via Boltz1 and those with top max ipSAE averaged across five diffusion models with 10 recycling steps are selected for this submission.
id: soft-lynx-oak

Multiple (2)
Medium (4), Strong (2)
True
15.4 kDa
142
id: misty-boar-onyx

Nipah Virus Glycoprotein G
None
71.99
True
16.2 kDa
149
id: soft-cat-vine

Nipah Virus Glycoprotein G
None
73.68
True
16.7 kDa
155
id: soft-shark-pearl

Nipah Virus Glycoprotein G
None
75.69
True
16.2 kDa
151
id: crimson-orca-marble

Nipah Virus Glycoprotein G
None
71.20
True
14.4 kDa
134
id: quick-falcon-jade

Nipah Virus Glycoprotein G
None
74.25
True
15.4 kDa
139
id: rapid-kiwi-ivy

Nipah Virus Glycoprotein G
None
83.28
True
15.9 kDa
149
id: scarlet-lynx-rose

Nipah Virus Glycoprotein G
0.32
63.69
--
14.2 kDa
135
id: lunar-panther-birch

Nipah Virus Glycoprotein G
0.62
68.71
--
15.9 kDa
146
id: solid-boar-frost

Nipah Virus Glycoprotein G
0.62
82.25
--
15.3 kDa
141