Docking Introduction and Walkthrough

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This walkthrough serves as a guide to performing a "re-dock" calculation using CHARMMing's docking module. A re-dock calculation involves removing a ligand molecule from a protein-ligand complex that has been crystallographically solved and re-docking it back into its binding site. This techniques is widely used to evaluate a performance of a docking algorithm. This walkthrough uses the ligand binding domain of the human nuclear receptor RXR alpha with the bound synthetic agonist compound BMS 649. This system is catalogued in the RCSB Protein Databank under the identification number 1MVC.

Step 1: Prepare the system for docking

The first thing to do is to import the system into the CHARMMing module for processing. To do this go to the "Submit Structure" submenu item under the "Structures" menu in the CHARMMing's main navigation menu. Once on the "Upload Structure" page, select "Retrieve PDB using a PDB ID" option. Below you will see the text box labeled PDB.org ID. Enter 1MVC and press "Submit Structure" button. See the image below.

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On the next screen check off segments a-bad, a-good and a-pro. Leave everything else as defaults and press "Submit".

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Once you see a message that your working structure has been created, click on the "Energy" submenu item under the "Calculations" menu in the CHARMMing's main navigation menu. On "Energy" screen, leave the form at the defaults and click "Calculate Energy".

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The screen will after some time display information such as the following:

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This means the energy calculation is compelete. At this point click on a "Minimization" submenu item under the "Calculations" menu in the CHARMMing's main navigation pane. On "Minimization" screen, leave the form at the defaults and click "Minimize".

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Step 2: Upload ligand

Now that the structure is undergoing the final minimization, the ligand for the re-docking can be uploaded into the system. To obtain co-crystallized ligand coordinates click on "Download Files" submenu item under the "Structures" menu in the CHARMMing's main navigation pane. There click on a "+" sign next to the "Segment setup files". There click on a file name that starts with "a-bad...." with the extention ".pdb". This file contains the coordinates of any non-protein, non-water moieties found in the crystal structure, which in this case is the ligand that we wish to re-dock. Clicking the file name will prompt you to download the file with coordinates in the pdb format. Save the file and note the location where you have saved it.

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Because CHARMMing's docking protocol at present accepts ligand coordinates only in .mol2, the downloaded ligand .pdb file needs to be converted to .mol2 format. Any conversion utility of your choosing can potentially be used to achieve this. For the purposes of this walkthrough however, OpenBabel program was used. For example, executing the following command at the prompt: babel -ipdb a-bad-xxxxx.pdb -omol2 1mvc_ligand.mol2 converts from .pdb to .mol2 coordinate files. In order to dock a ligand using CHARMMing's docking protocol, the ligand needs to be uploaded into the user's ligand library. To do so, click on a "Ligand Uplad" submenu under the "Docking" menu in the CHARMMing's main navigation pane. Once on the ligand upload screen, browse for the mol2 file of the ligand, enter information about the file, the source PDB structure (1MVC in this case), the ligand and any description you wish and click "Submit Structure File". All the parameters except for the file itself are optional, but we recommend filling out as much information as you can for ease of identifying the ligand once it is a part of the user's ligand library.

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Once the form clears, this means that the ligand was successfully uploaded and the interface is ready to accept any additional ligands.

Step 3: Docking

Now that the ligand is uploaded, the docking job can be initiated. However prior to doing so let's make sure that the minimization of the protein structure is complete. To do so look at the status box located at the bottom of the CHARMMing's main navigation pane. If it indicates that minimization is done then we can proceed to docking.

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To initiate a docking job navigate to the "Launch Docking Job" submenu under the "Docking" menu item in the CHARMMing's main navigation pane. There you will be prompte to select a working structure coordinates (protein coordinates). Select "Coordinates from minimization". Then select a-native-BM6.pdb as a definition of the binding site. Because this system contains no other co-crystallized ligands, this should already be selected by default. In the list of ligands, the drop-down should be set to "User Uploaded Ligands". The list will list all the ligands belonging to the user that were uploaded in the past. The most recently uploaded ligands are at the bottom, so scrolling may be needed to see the ligand uploaded as part of this walkthrough. Once the ligand is located, you can view its 3D structure by clicking on the "View" link next to the ligands description. To choose this ligand for docking, simply check the box in the rightmost column. Type the optional description of this docking job and click "Submit Docking Job" button.

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You will then be redirected to a screen with the confirmation that the job was submitted. You will also be given a link to an archive of the entire job's folder that you can download to run the job on resources other than CHARMMing's web server. Within a few seconds of the job submission you should see the status of the "dsfdocking" job as "Running" in the status box located at the bottom of the CHARMMing's main navigation pane. To monitor the progress of the job and view the results navigate to the "View Jobs/Results" submenu under the "Docking" menu item in the CHARMMing's main navigation pane. There you will see a list of all the jobs that have been run under this user account. The most recent jobs are displayed on top. To view the details of a particular job click either the job's ID or Description.

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The "Job Details" screen contains basic information about the job. If the job's current status is "Done", clicking the "View/Hide Results" link in the "Results" column of the job information section will toggle the "Results" section where any the poses of successfully docked ligands along with their scores are listed in the order of lowest DSFC Average score. User is given an option to view or download pose coordinates in mol2 format as well as view 3D rendering of the pose within the binding pocket. In addition this screen provides the list of ligands being docked as well as the docking procedure output and again the archive of the job for download.

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