Protein small-swan-oak

Yu-Hsin Chen / small-swan-oak

Type

Unknown

Ref

RFdiff-MPNN-JuncRING_12

Collections

Y[GEM x Adaptyv: RBX1 Binder Design Competition] Submission 1

AGEM x Adaptyv RBX1 Binder Competition: Main Submissions

Sequence (150 AA)

MKEKLIIIELRLAAAKPTTAVIKITVPGQKVEETRNFVQPLPTEVELELDLKNKNLLLNITARGSLVIIKVNMENGSLTVELTAEGERVTLILIVKAPEETKLEISFELGPEAPSEPIELKIEEFVGEKEEVEKKEKELLEKIKEEIYKE

Computational Metrics

Experimental Metrics

Structure prediction unavailable

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No experimental data

This protein hasn't been validated in the lab yet.

Design Method

This protein was designed using YCRFdiff-MPNN-JuncRING

Pipeline: RFdiffusion + SolubleMPNN (bias_AA C:-0.8) + Rosetta InterfaceAnalyzer + Boltz-2 validation
Target PDBs: junction+RING (res 15-108) from 2LGV_m0, 2LGV_m5, 1LDJ
ppi.hotspot_res: R24, R26, W35, I37 (junction anchors) + I44, W87, R91 (E2 critical)
Dual hard gate: junction_contacts == 0 → F=0 AND e2_essential_contacted == 0 → F=0
GP-UCB parameters: binder_length [60, 80, 100, 120, 150], noise_scale [0.0, 0.25, 0.5], mpnn_temp [0.05, 0.1, 0.2], hotspot_subset [all]
Cycles: 3 per target, 3 targets
Fitness: 20% f_e2 + 20% f_essential + 20% f_junction + 20% f_ddG + 10% f_dSASA + 10% f_hbonds
Result: highest avg score (0.730), zero-Cys in best designs, 100% filter pass, junction→E2 bridging confirmed