Drawing Schematic Of Protein-Protein Interactions

Question

[dimkal]

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.

[Pappu]

You can use pymol to show 3D structural interactions.

[dimkal]

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

Answer 1

[quentin.delettre]

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

[dimkal]

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

[quentin.delettre]

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.

[dimkal]

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?

[quentin.delettre]

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

[quentin.delettre]

Click on Prot-Prot.

http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=x081&pdb_type=UPLOAD&code=173341&template=interfaces.html&o=RESIDUE&l=1

Answer 2

[miquelduranfrigola]

Maybe Interactome3D is helpful.

[dimkal]

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

Answer 3

[Irsan]

cytoscape

[dimkal]

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.