Unraveling protein conformational plasticity with PROTEUS (opens in new tab)

Protein conformational plasticity underpins allosteric regulation, fold switching, and post-translational modification accessibility, yet no existing method can probe this property at the proteome scale without simulation. Here we show that SimpleFold, a flow-matching protein structure predictor, implicitly encodes conformational plasticity in its internal representations. By comparing per-residue embeddings between the sequence-only regime and the structure-converged regime of the denoising ...