{"id":622,"date":"2019-04-13T02:27:25","date_gmt":"2019-04-13T02:27:25","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/agfr\/?page_id=622"},"modified":"2019-10-30T23:13:59","modified_gmt":"2019-10-30T23:13:59","slug":"covalent-docking","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/agfr\/covalent-docking\/","title":{"rendered":"Covalent docking"},"content":{"rendered":"

This page was last updated on October 30th, 2019 at 11:13 pm<\/p>

Use case 5: covalent docking<\/h3>\n

In this scenario we have a receptor with a covalently attached ligand and we will prepare the receptor for docking covalent ligands. We will use chains A of PDB entry 3c9w. The file (3c9w_A_H.pdbqt) is available in the data associated with this tutorial \n\tADFRTutorialData.zip\t(11654 downloads\t)\n<\/a>\n.<\/p>\n

3c9w_A_H.pdbqt was created as follows:<\/strong><\/p>\n

    \n
  1. download 3c9w.pdb from\u00a0http:\/\/www.rcsb.org<\/a><\/li>\n
  2. extract chain A including the covalent ligand HMY1 but excluding water molecules using your favorite molecule editor (e.g. pymol) and save it as 3c9w_A.pdb<\/li>\n
  3. add hydrogen atoms using reduce command: ADFRsuite-1.0\/bin\/reduce 3c9w_A.pdb > 3c9w_A_H.pdb<\/li>\n
  4. generate the receptor PDBQT file, using the command:\u00a0ADFRsuite-1.0\/bin\/prepare_receptor -r 3c9w_A_H.pdb<\/li>\n<\/ol>\n

    run\u00a0ADFRsuite-1.0\/bin\/agfrgui<\/strong><\/em>\u00a0to start the Graphical User interface for these tutorials.<\/p>\n<\/div>