Evaluating native-like structures of RNA-protein complexes through the deep learning method
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DOI: 10.1038/s41467-023-36720-9
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- Andrew W. Senior & Richard Evans & John Jumper & James Kirkpatrick & Laurent Sifre & Tim Green & Chongli Qin & Augustin Žídek & Alexander W. R. Nelson & Alex Bridgland & Hugo Penedones & Stig Petersen, 2020. "Improved protein structure prediction using potentials from deep learning," Nature, Nature, vol. 577(7792), pages 706-710, January.
- Kengo Sato & Manato Akiyama & Yasubumi Sakakibara, 2021. "RNA secondary structure prediction using deep learning with thermodynamic integration," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
- Jun Li & Wei Zhu & Jun Wang & Wenfei Li & Sheng Gong & Jian Zhang & Wei Wang, 2018. "RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-18, November.
- Heena Khatter & Alexander G. Myasnikov & S. Kundhavai Natchiar & Bruno P. Klaholz, 2015. "Structure of the human 80S ribosome," Nature, Nature, vol. 520(7549), pages 640-645, April.
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