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. 2024 Jan 6;15:341. doi: 10.1038/s41467-023-44629-6

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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 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. 4 — a A given chemical reaction to demonstrate the use of TSDiff. b Visualization of the distribution of transition state (TS) conformations of the given reaction, using the t-distributed stochastic neighbor embedding (t-SNE) method based on the interatomic distances of the geometries. The geometries generated by TSDiff and the optimized results for them are indicated by dots and star-shaped dots, respectively. The reference TSs in the dataset are marked with a cross. The four values in this plot indicate the mean absolute error of the interatomic distances (D–MAE) between the two selected dots. The contours were plotted using kernel density estimation on the t-SNE transformed results. c The geometries and barrier heights corresponding to the nine different TS conformations, represented by the star-shaped dots in (b) with the same color as the box edges. All molecular geometries were plotted using PyMOL⁷¹.