We used Protein Hunter with Boltz-2, but replaced ProteinMPNN with fixed-backbone Caliby in the design pipeline. After obtaining a set of candidates with Boltz-2 ipSAE_asym (aligned on target, scored on binder) > 80, we predicted all complexes with AlphaFold3 (with MSA for target chain, no MSA for binder chain, and co-folded with 3 Zn2+). We then took all designs with AlphaFold3 ipSAE_asym > 80 and redesigned all sequences with ensemble-conditioned Caliby. Ensemble-conditioned Caliby refers to using partial diffusion with Protpardelle-1c to generate an ensemble of 32 backbones, followed by ensemble-conditioned sequence design conditioned on the target with SolubleCaliby. Both ensemble-conditioned designs and fixed-backbone designs were then predicted with binder-only and filtered for AlphaFold3 binder pLDDT > 80. We then bucketed by length and chose the best by AlphaFold3 ipSAE_asym. The final set of designs contains 50 fixed-backbone designs and 50 ensemble-conditioned designs.
id: radiant-seal-ash

RBX1
0.92
62.07
--
17.3 kDa
156
id: misty-swan-orchid

RBX1
0.90
47.47
--
17.6 kDa
155
id: violet-boar-fern

RBX1
0.93
83.18
--
17.9 kDa
157
id: misty-jaguar-snow

RBX1
0.86
78.45
--
19.6 kDa
176
id: rapid-wolf-fern

RBX1
0.91
57.65
--
16.4 kDa
148
id: crimson-wolf-stone
No preview available
--
--
--
--
--
176
id: calm-eagle-topaz
No preview available
--
--
--
--
--
170
id: frozen-vole-plume

RBX1
0.90
69.42
--
20.5 kDa
176
id: frozen-crow-crystal

RBX1
0.91
70.20
--
11.4 kDa
106
id: golden-crow-ruby

RBX1
0.94
75.61
--
17.7 kDa
159
id: silent-tiger-oak

RBX1
0.89
82.76
--
18.8 kDa
165
id: soft-gecko-lava

RBX1
0.93
77.74
--
12.9 kDa
116
id: scarlet-yak-ember

RBX1
0.90
76.86
--
19.0 kDa
160
id: green-gecko-cypress

RBX1
0.91
66.62
--
15.5 kDa
130
id: deep-owl-maple

RBX1
0.92
73.15
--
20.4 kDa
176
id: quick-boar-birch

RBX1
0.90
70.97
--
19.9 kDa
174
id: radiant-cobra-cedar

RBX1
0.89
81.94
--
19.9 kDa
175
id: amber-jaguar-willow

RBX1
0.90
69.39
--
19.3 kDa
172
id: soft-cat-flint

RBX1
0.87
75.09
--
20.2 kDa
176
id: swift-swan-snow

RBX1
0.91
45.54
--
12.2 kDa
108
id: scarlet-bison-birch

RBX1
0.92
81.23
--
19.7 kDa
176