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bioRxiv · 10.1101/2025.08.07.669087

HomRank: Homogeneous RNA Ranking for 3D Structure Evaluation

Li, L.·Yao, Y.·Martinovic|, I.·Kulkarni, M.·Pan, Y.·Huber, R. G.·Sick, M.
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Abstract

Leveraging rigorously curated RNA sequences and a novel ranking-based evaluation paradigm, we propose an improved pipeline for RNA 3D structure assessment. To enhance generalization, we construct a dataset comprising non-redundant single-chain RNA sequences from the PDB and apply unsupervised clustering to minimize data leakage. Based on this, we retrain the previous state-of-the-art method, ARES, to develop ARES+, which improves the top-1 success rate by 21% on the RNA Puzzles benchmark. To further boost near-native identification, we introduce HomRank, a homogeneous RNA ranking method that directly optimizes the selection of near-native conformations from candidate sets, resembling expert evaluation strategies. HomRank achieves 95% and 100% top-1 and top-5 success rates, respectively, significantly outperforming ARES+. These results demonstrate that carefully designed datasets and the expert-like selection paradigm can substantially improve the accuracy and robustness of RNA 3D structure assessment, offering a promising direction for deep learning-based RNA evaluation and near-native conformation selection.

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Li, L., Yao, Y., Martinovic|, I., Kulkarni, M., Pan, Y., Huber, R. G., Sick, M.. 2025-08-10. HomRank: Homogeneous RNA Ranking for 3D Structure Evaluation. https://doi.org/10.1101/2025.08.07.669087

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