DB5.5 · General PPI
80.2%
▲ +32.8 pts
vs vanilla Rosetta 47.4%
ProteinDock is a lightweight Rosetta layer that lifts top-1 docking reliability across general protein–protein and antibody–antigen benchmarks — with a pre-relax step, a single fa_elec × 1.5 reweight, and interface-aware refinement. No new score function. No new sampler.
Drop in as a layer over Rosetta's docking protocol. FastRelax each monomer, run local rigid-body sampling with an fa_elec × 1.5-reweighted REF2015, refine the interface, select top-1.
REF2015 · fa_elec × 1.5Take pose candidates from AlphaFold3 and Boltz-2, rescore by Rosetta interface energy under the same electrostatic reweight, and arbitrate across predictors. No re-sampling; a truncated ProteinDock scoring pass.
dG_interfaceFastRelax on each chain before docking. Removes internal strain that would otherwise force docking search away from the true basin.
fa_elec × 1.5. The 50 % boost to the electrostatic term recovers the polar, charge-driven interfaces that vanilla REF2015 systematically under-selects.
I_sc). No ensembles, no oracles, no reranker post-hoc.
ProteinDock: A physics-informed layer to improve protein–protein docking reliability. Manuscript in preparation.