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. 2024 Jan 27;15:810. doi: 10.1038/s41467-024-45028-1

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a AlphaFold2 predictions are strongly correlated with RoseTTAFold and trRosetta predictions. The confidence interval is estimated by 1000 bootstrap resamples and is shown in shadow. b Most de novo gene candidates might not have well-folded protein structures according to pLDDT, per-residue confidence score, and P(confident), which represents the percentage of residues that were confidently predicted by AlphaFold2 with pLDDT greater than 70. Boxplot (n = 555) is plotted with whiskers extending to ±1.5 × IQR. c Two examples of potentially well-folded de novo gene candidates: CG42590 and CG43070. In both cases, the core regions were predicted with very high confidence (blue). d The predicted structural models of the 19 potentially well-folded de novo genes retained highly similar structural folds during MD simulations with pairwise TM-score of representative structures close to or larger than 0.70. Source data is provided in the source data file.