Year: 2025
Type: preprint
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.
Authors: Youhan Lee, Shujun He, Toshiyuki Oda, G. John Rao, Yehyun Kim, Raehyun Kim, Hyunjin Kim, Cher Keng Heng, Danny Kowerko, Haowei Li, Hoa Nguyen, Arunodhayan Sampathkumar, Raúl Enrique Gómez, Meng Chen, Atsushi Yoshizawa, Shun Kuraishi, Kenji Ogawa, Shuxian Zou, Alejo Paullier, Bingkang Zhao, Huey-Long Chen, Tsu-An Hsu, Tatsuya Hirano, Wah Chiu, Jeanine G. Gezelle, Daniel Haack, Yibao Hong, Shekhar Jadhav, Deepak Koirala, Rachael C Kretsch, Anna Lewicka, Shanshan Li, Marco Marcia, Joseph Piccirilli, Boris Rudolfs, Yoshita Srivastava, Anna-Lena Steckelberg, Zhaoming Su, Navtej Toor, Liu Wang, Zi Yang, Kaiming Zhang, Jian Zou, David Baker, Shi-Jie Chen, Maggie Demkin, Andrew Favor, Alissa M Hummer, Chaitanya K. Joshi, Andriy Kryshtafovych, Emine Küçükbenli, Zhichao Miao, John Moult, Christian Munley, Walter Reade, Theo Viel, Eric Westhof, Sicheng Zhang, Rhiju Das
Institutions: Nvidia (United States), Texas A&M University, Uppsala University, University of Science and Technology of China, Google (United States), Centre National de la Recherche Scientifique, Howard Hughes Medical Institute, Institut Pasteur, University of Washington, University of Cambridge, Sichuan University, Chemnitz University of Technology, Science for Life Laboratory, SLAC National Accelerator Laboratory, Italian Institute of Technology, Yale University, University of California San Diego, University of Chicago, West China Hospital of Sichuan University, European Molecular Biology Laboratory, Mohamed bin Zayed University of Artificial Intelligence, Stanford Synchrotron Radiation Lightsource, Architecture et Réactivité de l'arN, Stanford Medicine, Toyama University Hospital, Institut de Biologie Moléculaire et Cellulaire, Zhejiang University-University of Edinburgh Institute, Peptidream (Japan), University of Toyama, Institute for Bioscience and Biotechnology Research, State Key Laboratory of Biotherapy, State Key Laboratory of Oral Diseases, Guangzhou Laboratory, Wenzhou Institute, University of Chinese Academy of Sciences, Université de Strasbourg, Universidad de Montevideo, University of Missouri, Columbia University, University of Maryland, Baltimore County, University of California, Davis, Stanford University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: National Science Foundation, Howard Hughes Medical Institute, U.S. Department of Energy, Nvidia, European Molecular Biology Laboratory, European Synchrotron Radiation Facility, National Natural Science Foundation of China, Technische Universität Dresden, National Institutes of Health, Office of Science, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, Argonne National Laboratory, SLAC National Accelerator Laboratory
Awards: G102163711, G1035064658, G107546177, G1313983767, G1664757510, G1713303463, G1722423347, G178916657, G2287611682, G2587019979, G2624333460, G262962599, G3075337988, G3886553587, G3927004650, G4269941704, G498139845, G513797252, Graduate Research Fellowship Program (GRFP), G5607048534, G5645718986, G6123861678, G6474251836, G6671297155, G6848031779, G6918803902, CAREER: Structural and mechanistic studies of RNA-mediated enteroviral genome replication, G880751848, New methods for computational modeling of RNA structures, Structure and Function of Non-Coding RNA, Structural Biology of Retrotransposition and pre-mRNA Splicing, Center for Structural Biology of HIV RNA, Understanding the antiviral roles of acellular RNA quality control pathway, G969889393, G993149817
OpenAlex ID: W7125529673