Hey there, has anybody seen any good ways to visualize specific protein-protein interactions? the only method I was able to find is a LigPlot+ tool called DIMPLOT. Though this is pretty close to what i want, i was wondering if there are any other know tools. Perhaps a way to display amino-acids as beads instead of actual 2d structure. These surfaces can get pretty complicated.
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dimkal
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A very schematic diagram can be generated with the pdbsum generate page.
If you enter a valid pdb code, you will see the output for it. If you upload your complex, you should have the output for it.
ok this was my result: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=x081&code=173341
where's the protein-protein interaction in the report?
Click on Prot-Prot.
If this is what you wanted, upvote the answer please.
Maybe Interactome3D is helpful.
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You can use pymol to show 3D structural interactions.
yes i'm aware of that, but i'm looking for a schematic-way, a simplified view. 3d views of surfaces can get complicated.