(1) We randomly selected three conformations of the target protein and identified three potential epitope regions following prior work. (2) Based on the preprocessed targets, we applied four versions of our sequence–structure binder co-design models—JointDiff-binder and JointDiff-x-binder—to generate candidate sequences with sizes of 100, 150, 200, and 250. For each combination of target, model, and size, we designed five sequences, resulting in a total of 720 sequences. (3) We evaluated the novelty and diversity of the designs. All sequences were sufficiently novel, with pairwise sequence identities below 0.3. (4) For each sequence, we used Boltz-2 to predict structures and the corresponding iPAE, and then computed the ipSAE. We generated three predictions per sequence and used the average ipSAE as the final score. (5) We ranked the sequences based on these scores. (6) Finally, we selected the top 100 sequences as our final submission.
id: vast-jaguar-rose

RBX1
None
37.83
False
10.9 kDa
100
id: gentle-swan-thorn

RBX1
None
63.11
True
11.3 kDa
100
id: rapid-bee-pine

RBX1
None
42.60
False
10.0 kDa
100
id: dark-kiwi-frost

RBX1
None
48.81
False
10.3 kDa
100
id: pale-panda-vine

RBX1
None
67.91
True
11.8 kDa
100
id: solid-bee-wave

RBX1
None
65.12
True
11.6 kDa
100
id: frozen-lion-sand

RBX1
None
32.58
False
10.6 kDa
100
id: hollow-kiwi-oak
No preview available
--
--
--
--
--
100
id: soft-orca-lava
No preview available
--
--
--
--
--
150
id: deep-deer-maple
No preview available
--
--
--
--
--
100
id: crimson-falcon-fern
No preview available
--
--
--
--
--
150
id: young-ibis-oak
No preview available
--
--
--
--
--
100
id: swift-kiwi-plume
No preview available
--
--
--
--
--
150
id: pale-jaguar-opal
No preview available
--
--
--
--
--
150
id: green-crane-frost
No preview available
--
--
--
--
--
100
id: rough-raven-dust
No preview available
--
--
--
--
--
150
id: ivory-mole-dust
No preview available
--
--
--
--
--
200
id: wild-bear-oak
No preview available
--
--
--
--
--
150
id: silver-owl-sand
No preview available
--
--
--
--
--
150
id: golden-cobra-cypress
No preview available
--
--
--
--
--
200
id: rough-hawk-iron
No preview available
--
--
--
--
--
100