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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 shape-restrained docking outputs (orange sticks) given the input shape (spheres) as compared to the target binding mode (grey sticks). Panels (A) and (B) represent the top 1 models generated by the shape- and the pharmacophore- based docking respectively for ada17 (ideal scenario), based on template 3b92. Panel (C) represents the best docking model generated in top 5 (orange) and overall (green, with an IL-RMSD value of 1.74 Å) for csf1r with the shape-based protocol, based on template 2i0v. Panel (D) represents the best docking model generated in top 5 for mk14 with the pharmacophore-based protocol, based on template 3 ha8. The color code for the pharmacophore spheres is the following: H-bond donor (green), H-bond acceptor (red), hydrophobic (yellow), aromatic (blue), and regular shape bead (white)