Pro-origami

Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.

Installing the Pro-origami software

The Pro-origami software for automatically generating protein structure cartoons is usually used via the Pro-origami server. However you can also install the software on your own system, should you need to (for example to make sure you can keep using it if the server is down, or to deal with structures that are large and cause gateway timeout errors on the server). A 64-bit Linux system is required. You do not need root (administrator) access on the system, and you can install it anywhere (somewhere under your home directory, for example). It only requires about 122 MB of disk space.

As described on the Pro-origami "About" page, Pro-origami consists of a large number of software components depending on many libraries, so the easiest way to install it is via the CDE (Code, Data, and Environment) package which you can download from http://munk.cis.unimelb.edu.au/pro-origami/proorigami-cde-package.tar.gz. I have also stored a copy at https://stivalaa.github.io/AcademicWebsite/software/proorigami-cde-package.tar.gz in case the original server is unavailable.

The instructions for doing this on the Pro-origami "About" page are very brief, and a little misleading, as third and final step shows the command

to make a cartoon from a PDB file in the /tmp directory. This works, however it is misleading as it makes it appear you can use a PDB file from anywhere. However this is not really true, as the CDE environment means that it will only work from some locations; specifically those that are not intercepted by the CDE system. So it will fail if you try to use a PDB file from under /home or /usr, for example. The simplest solution is to simply copy the PDB files you want into the same directory as the make_cartoon.sh.cde script (which will be your working directory when you run it).

Here is a transcript of a shell session showing exactly how to install and use Pro-origami on your own system, to create a cartoon for the cryoEM structure of glutamate dehydrogenase from Thermococcus profundus in complex with NADP, PDB identifier 8HIZ (the commands you enter are in bold):

Unfortunately, I no longer have access to log in to the Pro-origami server to fix problems or update documentation, and the CDE software seems to be no longer available anywhere, and links to its documentation on the Pro-origami "About" page no longer work. For more information on CDE, see:

Guo, P. J., & Engler, D. R. (2011, June). CDE: Using System Call Interposition to Automatically Create Portable Software Packages. In USENIX Annual technical conference (Vol. 21). https://www.usenix.org/legacy/event/atc11/tech/final_files/GuoEngler.pdf 

Citation

If you use Pro-origami in your research, please cite:

Dwyer, T., Marriott, K., Wybrow, M. (2009). Dunnart: A Constraint-Based Network Diagram Authoring Tool. In: Tollis, I.G., Patrignani, M. (eds) Graph Drawing. GD 2008. Lecture Notes in Computer Science, vol 5417, pp. 420-431. Springer, Berlin, Heidelberg. doi:10.1007/978-3-642-00219-9_41 

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. doi:10.1093/bioinformatics/btr575

Related software

As I have not been able to update the Pro-origami server since 2017, the links to related software there are out of date, and there are some new ones published since then. Here are some other software or servers that may potentially be used as alternatives to Pro-origami (or indeed in one case which incorporate Pro-origami themselves). 

• TopDraw 

  • Bond, C. S. (2003). TopDraw: a sketchpad for protein structure topology cartoons. Bioinformatics, 19(2), 311-312. doi.org/10.1093/bioinformatics/19.2.311 

• TOPS 

  • Westhead, D. R., Slidel, T. W., Flores, T. P., & Thornton, J. M. (1999). Protein structural topology: Automated analysis and diagrammatic representation. Protein Science, 8(4), 897-904. doi.org/10.1110/ps.8.4.897 

• PDBsum

  • Laskowski, R. A. (2001). PDBsum: summaries and analyses of PDB structures. Nucleic Acids Research, 29(1), 221-222. doi.org/10.1093/nar/29.1.221 

  • You can generate PDBsum analyses (including diagram) for an uploaded PDB file with PDBsum Generate.

  • A standalone version of PDBsum Generate is available to download for local installation from PDBsum1.

    • Laskowski, R. A. (2022). PDBsum1: A standalone program for generating PDBsum analyses. Protein Science, 31(12), e4473. doi.org/10.1002/pro.4473 

  • PDBsum generates secondary structure diagrams using PROMOTIF:

    • Hutchinson, E. G., & Thornton, J. M. (1996). PROMOTIF—a program to identify and analyze structural motifs in proteins. Protein Science, 5(2), 212-220. doi.org/10.1002/pro.5560050204 

  • and HERA:

    • Hutchinson, E. G., & Thornton, J. M. (1990). HERA—a program to draw schematic diagrams of protein secondary structures. Proteins: Structure, Function, and Bioinformatics, 8(3), 203-212. doi.org/10.1002/prot.340080303 

• PTGL 

  • Wolf, J. N., Keßler, M., Ackermann, J., & Koch, I. (2021). PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. Bioinformatics, 37(7), 1032-1034. doi.org/10.1093/bioinformatics/btaa706 

• 2DProts 

  • Hutařová Vařeková, I., Hutař, J., Midlik, A., Horský, V., Hladká, E., Svobodová, R., & Berka, K. (2021). 2DProts: database of family-wide protein secondary structure diagrams. Bioinformatics, 37(23), 4599-4601. https://doi.org/10.1093/bioinformatics/btab505 

  • https://gitlab.com/jhutar/2dprot 

• ProteoVision

  • Penev, P. I., McCann, H. M., Meade, C. D., Alvarez-Carreño, C., Maddala, A., Bernier, C. R., ... & Petrov, A. S. (2021). ProteoVision: web server for advanced visualization of ribosomal proteins. Nucleic Acids Research. 49(W1), W578-W588. https://doi.org/10.1093/nar/gkab351

    • "If an external 3D structure is provided instead using the ‘Upload a custom PDB’ option, ProteoVision takes it as an input for the Mol* Viewer, and generates a custom topology diagram using the Pro-Origami program (41,42)." [p. W582]

  • https://github.com/LDWLab/DESIRE 

• OverProt 

  • Midlik, A., Hutařová Vařeková, I., Hutař, J., Chareshneu, A., Berka, K., & Svobodová, R. (2022). OverProt: secondary structure consensus for protein families. Bioinformatics, 38(14), 3648-3650. https://doi.org/10.1093/bioinformatics/btac384 

  • https://gitlab.com/midlik/overprot 

[Formatted as bullet points as tables do not seem to be available in the "new" Google Sites.]