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. 2023 Jul 19;14:4361. doi: 10.1038/s41467-023-40045-y

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© The Author(s) 2023

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. 9 — Evaluation of AlphaFold models with a resolved experimental structure. A DockQ and B fraction of retrieved native contacts for the models generated with and without the usage of available 3D experimental templates of the monomer structures. N = 125 structural complex models computed for both conditions. The p-values have been computed with a two-sided Wilcoxon signed-rank test. Scatterplot of the DockQ of AlphaFold models computed using structural templates as a function of C the default score and D the pDockQ. Translucent bars represent 95% confidence intervals estimated with bootstrap. Filtered models contain only the residues with pLDDT ≥ 70. Binding energy of the filtered AlphaFold models estimated through Rosetta; E Alphafold complexes contact frequency heatmap for G_s (red scale), G_i/o (blue scale), G_q/11 (green scale) and G_12/13 (purple scale), each corresponding to a differently colored triangle: columns are GPCR positions in GPCRdb numbers, rows are G-protein positions in CGN numbers. Only contacts with frequency > 20% (over the number of unique complexes) are considered. The color intensity is proportional to the contact frequency. Experimental contacts are marked with a black asterisk; for E) all GPCR classes and F) only class A receptors. F ∆G binding (REU) predicted for AlphaFold-multimer complexes; p-values: Gs v.s. Gq/11 = 0.67; Gq/11 v.s. Gi/o = 1.55e-15; Gi/o v.s. G12/13 = 1; Gs v.s. Gi/o = 3.28e-11; Gq/11 v.s. G12/13 = 1.30e-5; Gs v.s. G12/13 = 4.06e-6; G Delta Solvent Accessible Surface Area (∆SASA); p-values: Gs v.s. Gq/11 = 1; Gq/11 v.s. Gi/o = 7.34e-16; Gi/o v.s. G12/13 = 1; Gs v.s. Gi/o = 5.52e-8; Gq/11 v.s. G12/13 = 3.45e-3; Gs v.s. G12/13 = 8.06e-3. The analysis considers n = 87 Gs, n = 265 Gq/11, n = 430 Gi/o, and n = 43 G12/13 structural complex models; H ∆G binding (REU) of complexes with class A, class B1, and class C receptors. The p-values have been computed with a two-sided Mann–Whitney U test with Bonferroni correction. ns P > 0.05; * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001. Boxplots show the median as the center and the first and third quartiles as the bounds of the box; the whiskers extend to the last data point within 1.5 times the interquartile range (IQR) from the box’s boundaries. Source data are provided as a Source Data file.