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. 2022 Nov 24;20(2):205–213. doi: 10.1038/s41592-022-01685-y

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, Distribution of the LEV score of all transplants obtained with 100% sequence identity (the validation set with n = 28,619 independent observations). 408 transplants (1%) with LEV score >2.5 are not shown for clarity. b, The local r.m.s.d. correlates with the LEV score in the validation set, Pearson correlation coefficient 0.51 (n = 8,039; mono-atomic transplants were not used (main text)). c, Distribution of the local r.m.s.d. of all transplants in the AlphaFill models as boxplots in 10% identity ranges. Boxes are based on 3,594,940; 3,866,810; 2,079,705; 1,005,953; 495,357; 369,307; 268,904 and 252,681 transplants, respectively, and extend from first to third quartile with the median as the middle line. Whiskers extend to 1.5 times the interquartile range. For clarity, 332,771; 333,325; 181,126; 79,594; 42,273; 34,634; 29,368 and 24,263 outliers, respectively, are not shown. Maximum values are 107.4, 82.1, 40.6, 37.1, 61.5, 44.4, 35.6 and 35.5 Å. d, The distribution of the TCS for all transplants in the AlphaFill models (n = 6,859,380). Mono-atomic transplants (5,170,409 compounds) are left out (main text). e, The TCS correlates with the LEV score in the validation set (n = 8,039; mono-atomic transplants were used (main text)), Pearson correlation coefficient 0.51. f, Comparison of the TCS before and after energy minimization for four subsets of the validation set (each with n = 50), illustrating that TCS improves for low until highest TCS by refinement.