Computational protocol: Benzimidazole inhibitors of protein kinase CK2 potently inhibit the activity of atypical protein kinase Rio1

Similar protocols

Protocol publication

[…] For molecular docking, we selected the X-ray structure of CK2 in complex with ANP (PDB ID: 3NSZ) and Rio1 in complex with ADP (PDB ID: 4OTP) as target proteins for the initial docking studies. All Mg2+ ions were removed in the 3NSZ and 4OTP experimental structures as well as all sulphates, co-solvents, water molecules, and original ligands. The structures were then minimized using YASARA Energy Minimization Server []. Autodock Tools v1.5.6 (The Scripps Research Institute) was used for charging the proteins as well as ligands. Docking calculations were performed with Autodock Vina v1.1.2 (The Scripps Research Institute) under default conditions []. During the docking calculations, all the protein residues were fixed and only the inhibitor atoms were allowed to move. Visualization of the binding site complexed with the docked ligand was performed by Maestro Suite and PyMOL v1.2 (Schrödinger) software. […]

Pipeline specifications