General
The complete course exists out of three parts, the introduction, OAH and 3DM, and the advanced course 3DM applied to GPCRs.
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For some exercises in this section, you'll need either PyMOL or YASARA installed which has the 3DM plugin. If you don't have YASARA or PyMOL or you are missing the 3DM functionality, please consult the installation instructions. Make sure you have the latest version installed before you start this exercise.
Index
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A: 3D numbers make life easy
In this section, we will explain the advantages of the number system used in 3DM. In addition, we guide you through the layout of the 3DM website and show you some handy features the website provides. Between instructions and information, there will be small exercises to learn how to navigate 3DM.
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There are many papers describing mutations in the human CAR and we still haven’t found a paper reporting a mutation that affects specificity. You might just read all these papers, but there is an easier way to do this using YASARA or PyMOL, as explained in the next section.
B: Easy visualization of data in structure files
In this second section, we look into visualization options of different structures and their characteristics. We will use YASARA or PyMOL to open the data we found in 3DM and use the 3DM plugin to visualize different data types. For this part, you'll need either PyMOL or YASARA installed which has the 3DM plugin. If you don't have either of these or when you are missing the 3DM functionality, please consult the installation instructions. Make sure you have the latest version installed before you start this exercise.
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Question: How would you normally find out the different binding points of inhibiting and activating proteins? |
C: Different search options and subset generation.
There are different search options available within 3DM to create a subset of sequences. In the "Search" menu we can search with different modules such as Search by keyword, BLAST, structures, or compounds. We can save a subset of all the sequences selected by the search options. We can access the subsets via the "Subsets" button in the top right, this will display the subset window. It is possible to create small 3DM systems of a selected subset in this side menu. All the 3DM options and scene visualizations are available for the smaller subsets. Below we explain how to generate and use the subsets.
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Inhibiting compounds compete with helix 12. Helix 12 docks to position 31 and 34 in the active state. If an inhibitor is bound it pushes away the complete 12th helix, towards the long helix starting at position 43 of 1G2NA. This relocation of helix 2 is such that the co-factor can’t bind anymore. |
D: Designing drugs with 3DM
Use "Search" → "Structures" from the side menu to find an androgen receptor structure with its natural ligand dihydrotestosterone bound in the ligand-binding pocket.
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