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How to save a PDB file of just the native ligand from the experimental structure, so you can overlay the native ligand structure with the docked ligand.
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Overlaying the docked poses with the native ligand
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Using ViewDock to look at the scores and poses of docked small molecule ligands in the target receptor
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Alternate way to select and delete a ligand from a protein structure - using the Cntrl + Left Click selection strategy
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Deleting the existing/experimental ligand from the structure before docking
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Draw the "box" in AutoDock Vina. Use a native or experimental ligand to help you locate and size the box.
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Open AutoDock Vina, specify receptor, ligand and output location
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Add a ligand to the Chimera session with the dock-prepped protein/receptor structure
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Saving the Chimera session. Don't forget to type out a .py suffix for your file name.
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Dock Prep of the Protein structure including charges
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Selecting and hiding protein chains and small molecules
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Saving the structure as Chem3D and *.pdb files
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Checking bond lengths and angles, optional MM2 calculation
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Drawing a structure in Chem3D
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