AlphaFold predictions of fold-switched conformations are driven by structure memorization
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DOI: 10.1038/s41467-024-51801-z
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- Georgios A. Pavlopoulos & Fotis A. Baltoumas & Sirui Liu & Oguz Selvitopi & Antonio Pedro Camargo & Stephen Nayfach & Ariful Azad & Simon Roux & Lee Call & Natalia N. Ivanova & I. Min Chen & David Pae, 2023. "Unraveling the functional dark matter through global metagenomics," Nature, Nature, vol. 622(7983), pages 594-602, October.
- Philipp Konrad Zuber & Kristian Schweimer & Paul Rösch & Irina Artsimovitch & Stefan H. Knauer, 2019. "Reversible fold-switching controls the functional cycle of the antitermination factor RfaH," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
- Patrick Bryant & Gabriele Pozzati & Arne Elofsson, 2022. "Author Correction: Improved prediction of protein-protein interactions using AlphaFold2," Nature Communications, Nature, vol. 13(1), pages 1-1, December.
- Yao Xia & Rongfeng Zou & Maxime Escouboué & Liang Zhong & Chengjun Zhu & Cécile Pouzet & Xueqiang Wu & Yongjin Wang & Guohua Lv & Haibo Zhou & Pinghua Sun & Ke Ding & Laurent Deslandes & Shuguang Yuan, 2021. "Secondary-structure switch regulates the substrate binding of a YopJ family acetyltransferase," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
- Patrick Bryant & Gabriele Pozzati & Arne Elofsson, 2022. "Improved prediction of protein-protein interactions using AlphaFold2," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
- Gabriel Monteiro da Silva & Jennifer Y. Cui & David C. Dalgarno & George P. Lisi & Brenda M. Rubenstein, 2024. "High-throughput prediction of protein conformational distributions with subsampled AlphaFold2," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Joseph W. Schafer & Lauren L. Porter, 2023. "Evolutionary selection of proteins with two folds," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Lauren L. Porter & Allen K. Kim & Swechha Rimal & Loren L. Looger & Ananya Majumdar & Brett D. Mensh & Mary R. Starich & Marie-Paule Strub, 2022. "Many dissimilar NusG protein domains switch between α-helix and β-sheet folds," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
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