We first used Boltzgen at a low batch size to determine the target hotspot and binder length with high success rate. Then we selected a suitable optimized approach and generated more binder backbones via RFdiffusion3 and Odesign to increase diversity. Following sequence design with ProteinMPNN/LigandMPNN and structure prediction via AlphaFold3/Protenix, we iterated the pipeline and scaled up the design batch size. Final filtering of high-quality predicted structures (with both high ipTM and ipSAE) was performed using Rosetta-ddg.
id: frozen-ant-opal

RBX1
0.39
90.56
--
11.0 kDa
100
id: noble-panther-willow

RBX1
0.05
87.89
--
11.2 kDa
99
id: jade-ibis-opal

RBX1
0.91
89.65
--
9.4 kDa
90
id: frozen-crane-opal

RBX1
0.90
89.72
--
9.5 kDa
90
id: ivory-ox-quartz

RBX1
0.91
88.45
--
9.6 kDa
90
id: young-zebra-cypress

RBX1
0.61
86.22
--
11.5 kDa
99
id: mellow-ox-pine

RBX1
0.89
88.41
--
9.7 kDa
91
id: radiant-quail-quartz

RBX1
0.02
86.67
--
11.4 kDa
99
id: solid-boar-orchid

RBX1
0.16
69.96
--
7.5 kDa
67
id: azure-panther-leaf

RBX1
0.70
87.35
--
11.4 kDa
99
id: ivory-panda-crystal

RBX1
0.21
86.39
--
11.2 kDa
99
id: rough-swan-stone

RBX1
0.50
74.95
--
7.5 kDa
67
id: shy-bison-maple

RBX1
0.43
89.83
--
11.1 kDa
100
id: deep-goat-granite

RBX1
0.22
88.00
--
11.3 kDa
99
id: lunar-lion-opal

RBX1
0.92
90.46
--
9.4 kDa
90
id: bright-falcon-ivy

RBX1
0.79
86.11
--
6.8 kDa
63
id: dark-crane-thorn

RBX1
0.83
87.42
--
11.4 kDa
99
id: soft-vole-lava

RBX1
0.87
87.29
--
10.8 kDa
98
id: mellow-swan-ruby

RBX1
0.52
88.39
--
11.4 kDa
99
id: brisk-crow-onyx

RBX1
0.12
87.84
--
11.3 kDa
99
id: misty-bat-pearl

RBX1
0.23
88.05
--
11.3 kDa
99