Our de novo peptide design strategy for targeting RBX1 integrates sequence generation, novelty screening, structural evaluation, and energetic ranking into a unified pipeline to efficiently identify high-confidence binders. We first generate a diverse set of peptide candidates of varying lengths (5–40 amino acids) using PepMind, a multimodal discrete diffusion model that co-generates peptide sequences and 3D coordinates conditioned on the RBX1 target. To ensure novelty and compliance with competition rules, peptides are filtered against UniRef50 using MMseqs2 to remove sequences exceeding 25% identity to known proteins, with clustering analysis confirming high sequence diversity among retained candidates. The filtered peptides are then docked to RBX1 using RAPiDock to produce complex conformations, which are evaluated for energetic favorability using both Rosetta and FoldX, discarding weak binders. Top-ranking peptides are further assessed for structural reliability and interface quality with AlphaFold3 metrics (pLDDT, PAE, ipTM), and final selection prioritizes peptides that simultaneously optimize sequence novelty, binding energetics, and structural confidence. This integrated, multi-stage approach ensures that our design process balances chemical and structural optimization with strict novelty constraints, providing a rational and efficient path from initial generation to high-quality candidate selection.
id: soft-bat-moss

RBX1
None
57.95
True
3.0 kDa
25
id: steady-lion-clay

RBX1
None
57.48
True
1.7 kDa
14
id: crimson-deer-bronze

RBX1
None
83.71
True
3.8 kDa
33
id: solid-moth-pearl

RBX1
None
51.40
True
3.2 kDa
28
id: misty-tiger-oak

RBX1
None
64.71
True
2.4 kDa
21
id: mellow-otter-lotus

RBX1
None
54.37
False
3.5 kDa
33
id: deep-ram-quartz

RBX1
None
75.49
True
4.2 kDa
35
id: calm-otter-lotus

RBX1
0.17
55.27
--
3.9 kDa
33
id: steady-orca-stone

RBX1
0.21
56.69
--
3.2 kDa
27
id: young-gecko-plume

RBX1
0.07
55.32
--
3.7 kDa
31
id: quiet-cobra-ember

RBX1
0.36
77.51
--
2.7 kDa
22
id: frozen-panda-lotus

RBX1
0.59
54.53
--
3.0 kDa
26
id: hollow-jaguar-vine

RBX1
0.08
55.62
--
2.3 kDa
20
id: strong-ant-orchid

RBX1
0.38
58.07
--
3.1 kDa
25
id: silent-ram-wave

RBX1
0.54
61.33
--
2.0 kDa
17
id: gentle-lion-stone

RBX1
0.41
81.87
--
3.4 kDa
29
id: rough-hawk-oak

RBX1
0.62
66.59
--
1.1 kDa
10
id: quiet-mole-stone

RBX1
0.21
70.34
--
2.2 kDa
19
id: gentle-hawk-oak

RBX1
0.13
48.59
--
4.3 kDa
39
id: deep-yak-topaz

RBX1
0.01
47.61
--
4.6 kDa
39
id: pale-quail-plume

RBX1
0.16
77.29
--
3.4 kDa
27