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. 2021 Aug 26;61(9):4807–4818. doi: 10.1021/acs.jcim.1c00796

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© 2021 The Authors. Published by American Chemical Society

Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).

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Illustration of the impact of the semi-flexible refinement on the docking model quality. Panel (A) shows the distribution of the ΔIL-RMSD between the models before and after semi-flexible refinement, computed as the IL-RMSD at it0, the IL-RMSD at it1 for a given model. The figure is divided into two parts: the left subpanel shows the distribution of ΔIL-RMSD for models that are acceptable at it1, the right subpanel shows the distribution of ΔIL-RMSD for models that are not acceptable at it1. Positive values in the distribution indicate better it1 performance. Panel (B) illustrates three cases with large IL-RMSD improvement between the model generated at it0 (blue) and the refined model at it1 (orange) as compared to the bound conformation in the reference structure (grey). Templates 2of4, 3bki, and 1kqu were used for cases lck, gria2, and pa2ga, respectively.