Dock Sampling

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Pose Sampling in DOCK

Don't get right DOCK pose? Well, this happens a lot... Docking is a complicated process, but it can be broken down to two main processes: scoring and sampling. This page is about sampling (in DOCK).

To investigate why you don't get the right DOCK pose (in the case you know the answer from a crystal structure), you can consider the following things:

1. Check if the bioactive conformation is sampled in docking. This is described here: http://wiki.uoft.bkslab.org/index.php/Screen3d 2. Dock the bioactive conformation rigidly. This is described here: http://wiki.uoft.bkslab.org/index.php/Multimol2db.py 3. Run score_opt on the bioactive conformation to get a score for the crystallographic pose of your ligand. This is described here:

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