Hi fellow structural biologists!
I'm currently trying to design diagrams to demonstrate the structural topology of a few proteins that I have (beta-sheet order), but I don't know what software or app people use to design them. I want to be able to manually make changes and annotate them myself as well, but I'm not sure what the standard used in structural biology is. If anybody could suggest some software or web apps that are good this this, I'd be very appreciative!
For clarity, the diagram type I'm describing can be seen on the left of the image I've attached.
Thank you!
Rob
Hi Amy Johnson
thanks for your suggestion! Unless I'm mistaken, Pymol can't generate the diagrams that I'm referring to (on the left of the picture I've attached), but is used for visualizing the molecules in various forms? I'm after something that can generate the type of diagram on the left of my attached file :)
Amy Johnson
I see, I will investigate the plug-ins further to try to find one that works for what I need. Thanks!
Dear Rob Barringer ,
This might be what you are looking for, TopDraw:
Bond, C. S. (2003). TopDraw: a sketchpad for protein structure topology cartoons. Bioinformatics, 19(2), 311-312.
It is used to provide the ‘mind-blowing’ cartoons I think you are looking for. See for example:
Komander, D., Lord, C. J., Scheel, H., Swift, S., Hofmann, K., Ashworth, A., & Barford, D. (2008). The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module. Molecular cell, 29(4), 451-464.
And example of combined use of Pymol and TopDraw:
Vaaje-Kolstad, G., Houston, D. R., Riemen, A. H., Eijsink, V. G., & van Aalten, D. M. (2005). Crystal structure and binding properties of the Serratia marcescens chitin-binding protein CBP21. Journal of Biological Chemistry, 280(12), 11313-11319.
Hope this helps.
Best regards.
Hi Rob Keller, thanks a lot for your suggestion, this is exactly what I was looking for!
Dear Rob Barringer,
You're welcome. I found another possible alternative, Pro-origami:
Stivala, A., Wybrow, M., Wirth, A., Whisstock, J. C., & Stuckey, P. J. (2011). Automatic generation of protein structure cartoons with Pro-origami. Bioinformatics, 27(23), 3315-3316.
Some examples are:
Article Architectures of Lipid Transport Systems for the Bacterial O...
Pruneda, J. N., Durkin, C. H., Geurink, P. P., Ovaa, H., Santhanam, B., Holden, D. W., & Komander, D. (2016). The molecular basis for ubiquitin and ubiquitin-like specificities in bacterial effector proteases. Molecular cell, 63(2), 261-276.
Good luck and best regards.
Hello Rob Barringer , you can also try Protter (http://wlab.ethz.ch/protter/start/).
Hi Robert Adamu Shey , thank you, this software looks very cool and useful, but unfortunately isn't the answer for the question that I posted. The question is regarding the diagram shown in the image attached to the question, which is a different definition of 'topology' to the topology that Protter assesses.
Hai Li Zhen Gong , I have found that the PDBsum server can create topology plots for you if you upload your .pdb structure:
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html
Alternatively, ProOrigami is capable of doing it also, as per Rob Keller suggestion:
http://munk.cis.unimelb.edu.au/pro-origami/
Personally I created my own manually using Biorender, which takes longer but I think looks very nice:
https://biorender.com
It is free to sign up and is great for illustrations generally. It also is online so you don't have to download anything, very easy to use.
Hi, Rob Barringer!
I would recommend Mind the Graph (mindthegraph.com), it's cheap, easy to use, and there are lots of illustrations, templates, and a poster maker!
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