Journal: Frontiers in Chemistry

Article Title: Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock

doi: 10.3389/fchem.2019.00709

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

Article Snippet: An AutoDock Vina virtual screening was also performed with the same targets as the CaverDock virtual screening.

Techniques: Software, Ligand Binding Assay, Extraction

Journal: Frontiers in Chemistry

Article Title: Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock

doi: 10.3389/fchem.2019.00709

Figure Lengend Snippet: Structure of cytochrome P450 17A1 with tunnels calculated using Caver and binding poses obtained by CaverDock. (A) Global view of tunnels—tunnel 1 (blue), tunnel 2A (red), tunnel 3 (green). (B) View of tunnels with no protein visualized. Each tunnel has the ligand bound in the minimum obtained from the CaverDock continuous trajectory calculation. (C) Tunnel 1 and minimum binding energy pose obtained from CaverDock (blue) and AutoDock Vina (black). (D) Tunnel 2A and minimum binding energy pose obtained by CaverDock (red) and AutoDock Vina (black). (E) Tunnel 3 and minimum binding energy pose obtained by CaverDock (green) and AutoDock Vina (black).

Article Snippet: An AutoDock Vina virtual screening was also performed with the same targets as the CaverDock virtual screening.

Techniques: Binding Assay

Journal: Frontiers in Chemistry

Article Title: Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock

doi: 10.3389/fchem.2019.00709

Figure Lengend Snippet: Structure of protein leukotriene A4 hydrolase/aminopeptidase with tunnels calculated using Caver and binding poses obtained by CaverDock. (A) Global view with tunnels LTA4 (blue) and PGP (red). (B) Tunnel LTA4 and minimum binding energy pose represented by balls and sticks obtained from CaverDock (blue) and AutoDock Vina (black). (C) Tunnel PGP and minimum binding energy pose represented by balls and sticks obtained from CaverDock (red) and AutoDock Vina (black).

Article Snippet: An AutoDock Vina virtual screening was also performed with the same targets as the CaverDock virtual screening.

Techniques: Binding Assay