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. 2024 Nov 11;16:126. doi: 10.1186/s13321-024-00923-z

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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. 12 — Pocket volume calculation algorithm. A PUResNet predicted pocket for PDB: 4PX2 [141]. Pocket residues are coloured in blue and have their side chains displayed; B an inclusion region is determined using the coordinates of the pocket residue atoms; C POVME 2.0 calculates the shape of the pocket defined by the residues and contained within the inclusion region; D The pocket shape is defined by a series of unit-volume (1 Å³) spheres. The volume of the pocket is calculated as the addition of the sphere volumes or the number of spheres within the pocket. Structure visualisation with PyMOL v2.5.2 [61]