This workflow implements a de novo protein binder design campaign targeting RBX1 using the Proteina-Complexa framework to generate large numbers of candidate protein binders. The pipeline starts with a prepared RBX1 structural region and performs computational generation of binder–target complexes while exploring different binder length ranges and interface targeting strategies. The generation stage uses multiple campaign configurations, including focused and expanded interface targeting modes, variable binder lengths, and different diffusion depths to balance structural diversity and design confidence. Each run produces predicted binder–target complex structures, evaluation outputs, and filtered candidate sets for further analysis. After candidate generation, a downstream validation stage is applied where selected binders are rescored using Boltz2 structural prediction, ipSAE interface confidence analysis, and PRODIGY binding affinity estimation. These tools help identify structurally stable binders with strong predicted interactions with the RBX1 target, enabling prioritization of high-confidence candidates for final submission.
id: radiant-moth-dust

RBX1
0.77
89.32
--
20.4 kDa
184
id: rough-panda-dust

RBX1
0.88
88.04
--
18.8 kDa
168
id: solid-cobra-dust
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RBX1
0.76
85.31
--
18.9 kDa
168
id: small-ant-onyx

RBX1
0.60
90.74
--
16.0 kDa
152
id: crimson-goat-ruby

RBX1
0.33
87.63
--
22.0 kDa
205
id: small-bear-vine

RBX1
0.85
91.98
--
20.7 kDa
195
id: silver-bat-topaz

RBX1
0.63
88.67
--
21.2 kDa
204
id: frozen-toad-leaf

RBX1
0.66
85.59
--
19.0 kDa
173
id: strong-heron-willow

RBX1
0.80
48.99
--
23.2 kDa
204
id: gentle-cobra-pine

RBX1
0.70
88.40
--
19.0 kDa
168
id: lunar-toad-rose

RBX1
0.70
87.51
--
18.6 kDa
165
id: vast-hawk-flint

RBX1
0.79
87.89
--
16.2 kDa
145
id: pale-zebra-sand

RBX1
0.63
88.91
--
17.1 kDa
153
id: scarlet-bear-pearl

RBX1
0.71
90.21
--
20.1 kDa
180
id: ivory-bison-cloud

RBX1
0.82
88.60
--
23.2 kDa
213
id: brisk-cat-plume

RBX1
0.00
82.48
--
24.2 kDa
215
id: azure-bear-willow

RBX1
0.73
88.35
--
20.0 kDa
178
id: deep-yak-ash

RBX1
0.48
87.44
--
23.2 kDa
206
id: bright-quail-rose

RBX1
0.55
82.51
--
18.6 kDa
165
id: azure-bear-plume

RBX1
0.47
86.27
--
22.4 kDa
212
id: jade-swan-ivy

RBX1
0.70
81.89
--
20.1 kDa
176