Computational protocol: Discovery of a small-molecule binder of the oncoprotein gankyrin that modulates gankyrin activity in the cell

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Protocol publication

[…] Docking experiments were performed using a blind docking approach and several software packages based on different algorithms. These include AutoDock Vina version 1.1.2 (http://vina.scripps.edu/), AutoDock 4.2 (http://autodock.scripps.edu/) and EADock DSS implemented in the SwissDock server (http://www.swissdock.ch/). In each case, docking was performed as three independent runs to assess reproducibility and only the lowest energy pose was considered for each case. For detailed inspection and analyses of the docked poses, ligand interaction diagrams were generated using LigPlot + version 1.4 and Protein-ligand interaction profiler (PLIP). FTMAP server (http://ftmap.bu.edu/) was used for predicting the hot spots for ligand binding on the gankyrin surface. […]

Pipeline specifications