ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings

Josef Hanke; Sebastian Pujalte Ojeda; Shengyu Zhang; Werngard Czechtizky; Leonardo De Maria; Michele Vendruscolo

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arXiv · 2603.23583

ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings

Josef Hanke·Sebastian Pujalte Ojeda·Shengyu Zhang·Werngard Czechtizky·Leonardo De Maria·Michele Vendruscolo

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Abstract

The accurate prediction of protein-RNA binding affinity remains an unsolved problem in structural biology, limiting opportunities in understanding gene regulation and designing RNA-targeting therapeutics. A central obstacle is the structural flexibility of RNA, as, unlike proteins, RNA molecules exist as dynamic conformational ensembles. Thus, committing to a single predicted structure discards information relevant to binding. Here, we show that this obstacle can be addressed by extracting pre-structural embeddings, which are intermediate representations from a biomolecular foundation model captured before the structure decoding step. Pre-structural embeddings implicitly encode conformational ensemble information without requiring predicted structures. We build ZeroFold, a transformer-based model that combines pre-structural embeddings from Boltz-2 for both protein and RNA molecules through a cross-modal attention mechanism to predict binding affinity directly from sequence. To support training and evaluation, we construct PRADB, a curated dataset of 2,621 unique protein-RNA pairs with experimentally measured affinities drawn from four complementary databases. On a held-out test set constructed with 40% sequence identity thresholds, ZeroFold achieves a Spearman correlation of 0.65, a value approaching the ceiling imposed by experimental measurement noise. Under progressively fairer evaluation conditions that control for training-set overlap, ZeroFold compares favourably with respect to leading structure-based and leading sequence-based predictors, with the performance gap widening as sequence similarity to competitor training data is reduced. These results illustrate how pre-structural embeddings offer a representation strategy for flexible biomolecules, opening a route to affinity prediction for protein-RNA pairs for which no structural data exist.

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Josef Hanke, Sebastian Pujalte Ojeda, Shengyu Zhang, Werngard Czechtizky, Leonardo De Maria, Michele Vendruscolo. 2026-03-24. ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings. https://arxiv.org/abs/2603.23583

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