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. 2019 Oct 29;7:709. doi: 10.3389/fchem.2019.00709

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Copyright © 2019 Pinto, Vavra, Filipovic, Stourac, Bednar and Damborsky.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Workflow of virtual screening using CaverDock. (1) Receptor and (2) ligand specification follow established protocols of the software tool AutoDock (Morris et al., 2009). (3) Identification of protein tunnels using Caver (Chovancova et al., 2012). (4) Tunnel discretization and sequential ligand binding study using CaverDock (Filipovic et al., 2019; Vavra et al., 2019). (5) Analysis of docking trajectories and energy profiles, extraction of energy barriers and protein-ligand complexes possessing the lowest energies.