Template-based RNA structure prediction advanced through a blind code competition

Lee, Y.; He, S.; Oda, T.; Rao, G. J.; Kim, Y.; Kim, R.; Kim, H.; Heng, C. K.; Kowerko, D.; Li, H.; Nguyen, H.; Sampathkumar, A.; Enrique Gomez, R.; Chen, M.; Yoshizawa, A.; Kuraishi, S.; Ogawa, K.; Zou, S.; Paullier, A.; Zhao, B.; Chen, H.-L.; Hsu, T.-A.; Hirano, T.; Gezelle, J. G.; Haack, D.; Hong, Y.; Jadhav, S.; Koirala, D.; Kretsch, R. C.; Lewicka, A.; Li, S.; Marcia, M.; Piccirilli, J.; Rudolfs, B.; Srivastava, Y.; Steckelberg, A.-L.; Su, Z.; Toor, N.; Wang, L.; Yang, Z.; Zhang, K.; Zou, J.; Baker, D.; Chen, S.-J.; Chiu, W.; Demkin, M.; Favor, A.; Hummer, A. M.; Joshi, C. K.; Kryshtafovyc

doi:10.64898/2025.12.30.696949

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bioRxiv · 10.64898/2025.12.30.696949

Template-based RNA structure prediction advanced through a blind code competition

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Abstract

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores within statistical error of the winners of the recent CASP16 competition. Unexpectedly, the top Kaggle strategy involved a pipeline for discovering 3D templates, without the use of deep learning. We integrated this template-modeling pipeline and other Kaggle strategies to develop a single model RNAPro that retrospectively outperformed individual Kaggle models on the same test set. These results suggest a growing importance of template-based modeling in RNA structure prediction.

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Lee, Y., He, S., Oda, T., Rao, G. J., Kim, Y., Kim, R., Kim, H., Heng, C. K., Kowerko, D., Li, H., Nguyen, H., Sampathkumar, A., Enrique Gomez, R., Chen, M., Yoshizawa, A., Kuraishi, S., Ogawa, K., Zou, S., Paullier, A., Zhao, B., Chen, H.-L., Hsu, T.-A., Hirano, T., Gezelle, J. G., Haack, D., Hong, Y., Jadhav, S., Koirala, D., Kretsch, R. C., Lewicka, A., Li, S., Marcia, M., Piccirilli, J., Rudolfs, B., Srivastava, Y., Steckelberg, A.-L., Su, Z., Toor, N., Wang, L., Yang, Z., Zhang, K., Zou, J., Baker, D., Chen, S.-J., Chiu, W., Demkin, M., Favor, A., Hummer, A. M., Joshi, C. K., Kryshtafovyc. 2025-12-30. Template-based RNA structure prediction advanced through a blind code competition. https://doi.org/10.64898/2025.12.30.696949

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