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. 2022 Apr 5;5:316. doi: 10.1038/s42003-022-03261-8

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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. 5 — Four protein structure pairs with the scores by 3DZD-NN and 3DZD are shown. The main-chain atom representation was used for these comparisons. The two pairs on panel a and b are cases where 3DZD did not recognize them as the same fold (i.e. false negative) but 3DZD-NN did. a d4rxfa1 and d3mana_ belong to the TIM beta/alpha-barrel (SCOP code: c.1). 3DZD-NN had a probability score of 0.99, i.e. very confident that these two structures belong to the same fold while 3DZD had a score of 0.082, below the detection threshold of 0.1. b d5mwnf1 and d4lpvb1, belong to Immunoglobulin-like beta-sandwich (b.1). Panel c and d shows two pairs, where 3DZD-NN correctly detected that the two structures have different folds while 3DZD had a score above the threshold of 0.1 and thus considered them as the same fold. Fold assignment of the four structures in SCOP are as follows: c, d1bvia_: Microbial ribonucleases (d.1); d1v8bd1: NAD(P)-binding Rossmann-fold domains (c.2); (d), d4pjhg2: Immunoglobulin-like beta-sandwich (b.1); d4z93a_: Bromodomain-like (a.29).