Intro
Welcome to the 3DM tutorial. A 3DM system is a data integration platform, we collect and integrate data about a protein superfamily.
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The lighter coloured residues are the variable regions and the bright-coloured ones are core regions. Keep in mind that only the aligned parts of the variable regions are displayed so you often don't see the full sequence in this view.
System info
Let's now have a look at the system info page - you can find a link in the menu on the left. This shows you an overview of the system, and gives you an idea of how much data there is.
Alignment statistics
Let's now navigate to the alignment statistics page, which you can access from the menu on the left side of the page.
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Go to the Visualize page from the menu, and click on the structures tab. From the templates menu select the 3VNNA 3W5OA structure - this is the template of the subfamily where our protein of interest is aligned. From the other tabs you can choose what data do you want to see mapped onto the structure - by default the residues with highest conservation and with highest correlated mutation score will be highlighted.
Go to the contacts tab and click on the checkbox in the top row in the DNA/RNA Contacts table (by clicking on the checkbox in the top row you toggle between selecting and deselecting all positions). Now click on the VISUALIZE IN YASARA button and a yasara scene with the selected data mapped onto the 1VS0A the 3W5OA structure will be downloaded.
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In the case of search proteins by position motif, we're looking for specific motifs on specific positions - for example we might want to find all proteins that have an aspartate on alignment position 242 and a lysine on alignment position 364
Virus-X proteins
Virus-X proteins are proteins that are added to the system through the Virus-X pipeline, they're only accessible for the Virus-X users.
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For now there is just one protein, but later on we'll be adding more proteins from the Bielefeld's webserver.
Advanced
Numbering schemes
You can simplify your work with the protein of interest even more by creating a custom numbering scheme - that will cause the alignment positions to be renumbered to match the residue numbering of your protein.
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