I am an early beta-user of the Synthyra PDE: an iterative, GA-driven pipeline for protein engineering that runs entirely on sequence-only models. It leverages diffusion pLMs to generate a massive starting population, then scores them through multiple cycles of selection using their custom pLM-based oracles. These oracles score for everything from PPI probability and binding affinity to standard stuff like foldability and solubility. For this specific run I set up the hyperparameters in an attempt to conduct many crossovers between the known Human protein interactors (Ephrin B2/B3) with the m102 antibody chains. I started with 10K variants went for 100 optimization steps. For the final screening I used Boltz-2 to calculate ipSAE in line with the competition's key metric.
id: ivory-bat-iron

Nipah Virus Glycoprotein G
0.81
75.30
--
20.3 kDa
182
id: radiant-kiwi-stone

Nipah Virus Glycoprotein G
0.78
79.38
--
20.3 kDa
182
id: green-orca-vine

Nipah Virus Glycoprotein G
0.78
76.79
--
20.0 kDa
182
id: solid-bear-granite

Nipah Virus Glycoprotein G
0.77
73.99
--
20.2 kDa
182
id: green-crane-pine

Nipah Virus Glycoprotein G
0.77
77.15
--
20.2 kDa
182
id: gentle-zebra-marble

Nipah Virus Glycoprotein G
0.77
78.65
--
20.0 kDa
182
id: steady-bee-reed

Nipah Virus Glycoprotein G
0.75
77.86
--
20.2 kDa
182
id: frozen-boar-pearl

Nipah Virus Glycoprotein G
0.74
84.05
--
20.2 kDa
182
id: silent-tiger-opal

Nipah Virus Glycoprotein G
0.70
76.41
--
20.4 kDa
182
id: vast-bat-ember

Nipah Virus Glycoprotein G
0.65
82.90
--
20.0 kDa
182