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Femke Kopmels

Femke Kopmels

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General

The complete course exists consists out of three parts:

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Question 25

Select a couple of structures and ligands. Then add positions, select the Correlated mutations tab and select the top five correlated mutations. From the "Conservation" select all residues >90% conserved. From the "Contacts" tab select all positions make at least 100 contacts with a ligand. Click on "visualize selection in Yasara" or "visualize selection in Pymol" and open the resulting file. Did you get back what you expected?

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In this picture the first three templates were selected, the top five correlating positions, the first three ligands and all positions >90% conserved. You can see that the correlated mutation nicely surround the ligands located inside the GPCRs.

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Question 30

  • Go to the "correlated mutations" option in 3DM and use the keyword specificity in the "Literature & Mutation" window with a keyword cut-off of 1. Make sure you have the GPCR class A selected. Open the hotspot basket tool and select a NEW hotspot basket. Select the 9 positions of the sub-network that contains mutations reported to effect specificity upon mutation. Click on the "add to hotspots" button

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    to store these specificity related mutations in a NEW basket. Give it a logical name and save it. We will use it later on.

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