Drawing Schematic Of Protein-Protein Interactions
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10.8 years ago
dimkal ▴ 730

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.

DIMPLOT

visualization amino-acids • 7.2k views
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You can use pymol to show 3D structural interactions.

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yes i'm aware of that, but i'm looking for a schematic-way, a simplified view. 3d views of surfaces can get complicated.

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10.8 years ago

A very schematic diagram can be generated with the pdbsum generate page.

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can you please point me to the output? i submitted an example on the site, but still waiting for results to be emailed.

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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.

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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?

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If this is what you wanted, upvote the answer please.

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10.8 years ago

Maybe Interactome3D is helpful.

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it's good for showing networks of protein-protein interactions, but not specific interactions, on amino-acid level.

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10.8 years ago
Irsan ★ 7.8k

cytoscape

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that's not exactly what i'm requesting. I'm not interested in representing networks of protein interactions, but protein-protein surfaces, with specific amino-acids contacts.

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