{"id":936,"date":"2019-04-18T19:10:40","date_gmt":"2019-04-18T19:10:40","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/adfr\/?page_id=936"},"modified":"2019-04-18T21:21:06","modified_gmt":"2019-04-18T21:21:06","slug":"tutorial-covalent","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/adfr\/tutorial-covalent\/","title":{"rendered":"tutorial covalent"},"content":{"rendered":"

Docking a covalently bound ligand<\/h3>\n

In this tutorial we illustrate how to re-dock the native covalent ligand of PDB id 3c9w.\u00a0Both, the receptor (3cw9.pdbqt) and ligand (3c9w_ligandWithSideChain_random.pdbqt<\/span>) are available in the data file associate with this tutorial.<\/p>\n

For covalent docking, the receptor and covalent ligand need to share 3 atoms as sown below. 2 atoms (green) for the covalent bond and 1 atom (yellow) is an anchor atom on the receptor side. These atoms are used to transform the ligand into place with respect to the receptor to create the covalent bond.<\/p>\n

NOTE: for covalent docking no translational points are needed as the ligand is positioned in the docking box using the covalent bond.<\/p>\n

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In this tutorial you will learn<\/strong>:<\/p>\n