Evaluating native-like structures of RNA-protein complexes through the deep learning method

Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng and Yunjie Zhao ()
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Chengwei Zeng: Central China Normal University
Yiren Jian: Dartmouth College
Soroush Vosoughi: Dartmouth College
Chen Zeng: The George Washington University
Yunjie Zhao: Central China Normal University

Nature Communications, 2023, vol. 14, issue 1, 1-9

Abstract: Abstract RNA-protein complexes underlie numerous cellular processes, including basic translation and gene regulation. The high-resolution structure determination of the RNA-protein complexes is essential for elucidating their functions. Therefore, computational methods capable of identifying the native-like RNA-protein structures are needed. To address this challenge, we thus develop DRPScore, a deep-learning-based approach for identifying native-like RNA-protein structures. DRPScore is tested on representative sets of RNA-protein complexes with various degrees of binding-induced conformation change ranging from fully rigid docking (bound-bound) to fully flexible docking (unbound-unbound). Out of the top 20 predictions, DRPScore selects native-like structures with a success rate of 91.67% on the testing set of bound RNA-protein complexes and 56.14% on the unbound complexes. DRPScore consistently outperforms existing methods with a roughly 10.53–15.79% improvement, even for the most difficult unbound cases. Furthermore, DRPScore significantly improves the accuracy of the native interface interaction predictions. DRPScore should be broadly useful for modeling and designing RNA-protein complexes.

Date: 2023
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DOI: 10.1038/s41467-023-36720-9

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