Protein binder scoring head-to-head: ipDAE consistently strong, OpenDDE+ipTM surprisingly good at 80% PPV
AllThingsApx · x · 2026-10-31
btnaughton shares a quick comparison of ipSAE vs ipDAE vs ipTM interface scores across folding models. Using Decade's ProteinBase benchmark (200 experimentally measured binders + 200 nonbinders, 28 targets, 3 structure predictors, ranking each method's top 10% by PPV), ipDAE (used by BindCraft2) is consistently strong at 72.5–80% PPV, while OpenDDE+ipTM is surprisingly good at 80% — robust across thresholds. Consensus ensembles of all three models help less than expected (72.5–75%).
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