For this competition, I adopted a sequence optimization strategy starting from known binder mAbs converted to scFv format. I utilized the AntiBERTy language model to obtain per-residue pseudo-log-likelihoods (PLL). By calculating the delta PLL for every possible substitution relative to the wildtype, I identified highly favorable mutations specifically within the framework regions to sample 10,000 combinatorial designs, enforcing at least 10 mutations per sequence. From there, I implemented a multi-stage filtering pipeline to identify the most promising candidates. I ranked the initial library using a combined score from AntiBERTy and IgLM, narrowing the pool to the top 100 sequences that exhibited high scores. To prioritize binding capability, I re-ranked these finalists using an ESM-2 model that I fine-tuned specifically to predict affinity for the given binder-target pairs. I selected the top 10 designs based on the fine-tuned ESM-2 predictions. These final candidates were checked by modeling the binder-target complex using both AlphaFold3 and Boltz-2.
id: ivory-dove-cypress

Nipah Virus Glycoprotein G
0.30
75.96
--
26.6 kDa
250
id: misty-falcon-ember

Nipah Virus Glycoprotein G
0.21
81.69
--
26.7 kDa
250
id: crimson-heron-vine

Nipah Virus Glycoprotein G
0.00
80.35
--
26.7 kDa
250
id: green-gecko-willow

Nipah Virus Glycoprotein G
0.05
81.06
--
26.8 kDa
250
id: frozen-crane-dust

Nipah Virus Glycoprotein G
0.13
75.30
--
26.7 kDa
250
id: brisk-bison-cloud

Nipah Virus Glycoprotein G
0.01
81.92
--
26.7 kDa
250
id: deep-fox-granite

Nipah Virus Glycoprotein G
0.02
80.86
--
26.6 kDa
250
id: silent-bee-quartz

Nipah Virus Glycoprotein G
0.52
78.84
--
26.6 kDa
250
id: frozen-gecko-opal

Nipah Virus Glycoprotein G
0.11
82.63
--
26.8 kDa
250
id: strong-ox-topaz

Nipah Virus Glycoprotein G
0.20
77.34
--
26.6 kDa
250