Ensemble-Aware Structural Encoding (EASE): Conditioning Protein Encoders on Peptide Conformational Ensembles

Abstract

Protein foundation models provide transferable representations for downstream peptide prediction tasks. However, existing representations typically reduce a peptide to a single sequence or structure, which may miss conformational variability relevant to key peptide properties, including antibacterial activity, hemolysis, toxicity, stability, and binding. For example, protease resistance correlates more strongly with conformational dynamics measured by hydrogen exchange than with average helicity. Therefore, we introduce Ensemble-Aware Structural Encoding (EASE), a framework for effectively extracting structural information from conformational ensembles for peptide representation. To extract useful information from noisy conformers, EASE selects central conformers representing a peptide's major structural states and fuses their individual representations with a permutation-invariant operator to produce a peptide-level representation for downstream prediction. We then evaluate our framework on six peptide property-prediction tasks under leakage-controlled splits. Against matched single-structure baselines, EASE improves performance consistently on six tasks with a mean absolute gain of about 3.0% across two structural encoders. Gains keep growing as we add conformers through K=20. A single peptide conformer therefore provides a limited basis for structural representation, whereas our framework distilling and fusing multiple conformers yields a more informative representation.