About 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.

The cartoons are drawn in a style similar to those that might be drawn manually using a tool such as Charles Bond's TopDraw program, rather than the purely topological style such as those drawn by TOPS or PTGL, or the detailed hydrogen bonding diagrams drawn by HERA (PROMOTIF), from which the cartoons available in PDBsum are derived.

Search

Note: This information is reproduced in a help pop-up on the Interactive SVG pages.

Pro-origami can also be used as a query interface to a substructure search program. The selected SSEs in the cartoon will be used as a substructure query against the the ASTRAL SCOP 1.75 PDB-style genetic domain 95% sequence identity filtered subset. The list of structures will be returned sorted with the best hit at the top. The SA Tableau Search button will run SA Tableau Search with 4096 restarts, for accurate but slower searches. The Fast SA Tableau Search button will run SA Tableau Search with 128 restarts, for faster but less accurate searches. The QP Tableau Search button will run the older QP Tableau Search program, also for slower but reasonably accurate searches.

SA Tableau Search and QP Tableau Search will queue a batch job and return a link that can be checked for the results; this could take many hours depending on the query and the load on the server. The Fast SA Tableau Search will run the query immediately and return the results directly to your browser; this should only take a few minutes at most.

Reference

Pro-origami is part of a research project involving A. Stivala, Dr. A. Wirth, Prof. P. Stuckey (University of Melbourne, Australia), Dr. M. Wybrow and Prof. J. Whisstock (Monash University, Australia).

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

A. Stivala, M. Wybrow, A. Wirth, J. Whisstock and P. Stuckey 2011 Automatic generation of protein structure cartoons with Pro-origami Bioinformatics 27(23):3315-3316 doi:10.1093/bioinformatics/btr575

If you use the SA Tableau Search feature, please also cite:

A. Stivala, P. Stuckey and A. Wirth 2010 Fast and accurate protein substructure searching with simulated annealing and GPUs BMC Bioinformatics 11:446

If you use the QP Tableau Search feature, please also cite:

A. Stivala, A. Wirth and P. Stuckey 2009 Tableau-based protein substructure search using quadratic programming BMC Bioinformatics, 10:153

Acknowledgments

Pro-origami uses the BioPython library. It makes use of several other software programs in generating cartoons.

• Dunnart: The Dunnart constraint-based diagram editor written by Michael Wybrow is used to layout the cartoons. The reference for Dunnart is: Tim Dwyer, Kim Marriott, and Michael Wybrow. Dunnart: A constraint-based network diagram authoring tool. In Proceedings of 16th International Symposium on Graph Drawing (GD'08), LNCS 5417, pages 420–431. Springer-Verlag, 2009.
• Inkscape: The open-source Inkscape scalable vector graphics editor is used to render the SVG into other image formats.
• DSSP: DSSP is used to assign secondary structure and find H bonds. The reference for DSSP is: Kabsch, Wolfgang and Sander, Christian. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-2637.
• STRIDE: STRIDE can also be used to assign secondary structure and find H bonds. The reference for STRIDE is: Frishman D, Argos P. Knowledge-Based Protein Secondary Structure Assignment Proteins: Structure, Function, and Genetics 23:566-579 (1995)
• DDOMAIN: DDOMAIN is used to divide protein structures into domains. The reference for DDOMAIN is: Zhou, Xue, Zhou 2007 DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Science 16:947-955.
• A CATH CDF file may also be used to identify protein domains. The reference for CATH is: Pearl et al. 2005. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research 33(database issue):D247-D251
• The interactive SVG uses the carto:net mapApp library and related SVG utilities.

• The pan and zoom functions in the SVG are implemented with the SVGPan library by Andrea Leofreddi.
• The CSS stylesheet for Proorigami was loosely based on the CSS Zen Garden sample style template.
• The interactive 3D view of the structure is provided by Jmol: an open-source Java viewer for chemical structures in 3D.
• The implementation of QP Tableau Search used here makes use of the HSL 2007 MA57 package for solving sparse symmetric indefinite linear systems.
• The action icons on the Pro-origami homepage are from the open-source Nuvola icon set.

Download

You can install and run Pro-origami on your own system should you wish to do so. Pro-origami consists of two main components: the Python scripts which you can download from ptgraph.tar.gz, and the Dunnart constraint-based diagram editor which can be downloaded from the Dunnart homepage. You must first install BioPython. You will also need either DSSP or STRIDE.

A copy of both Pro-origami and Dunnart, along with the protein structure search programs and the cartoons generated from the ASTRAL SCOP 1.75 database protein domains, and the HTML and scripts, as running on this server, is available from proorigami-prod.tar.gz (nearly 500 MB compressed, 1.5 GB when uncompressed). You will still need to install BioPython (note this server is using Python 2.4.3 and BioPython 1.53), as well as DSSP or STRIDE.

Because Pro-origami uses BioPython and Dunnart and several other software packages, each of which has its own further dependencies, getting it all installed and working can be difficult. Therefore, we have provided a CDE package which can be downloaded from proorigami-cde-package.tar.gz. This CDE package was created by running the make_cartoon.sh script on this server, which is a 64 bit Linux server, so that it will run on any 64 bit Linux system. Just download and run the following commands:

     tar zxf proorigami-cde-package.tar.gz
     cd proorigami-cde-package/cde-root/home/proorigami
     ./make_cartoon.sh.cde /tmp/pdb1qlp.ent.gz
     

(where /tmp/pdb1qlp.ent.gz is any PDB file you want to generate a cartoon for). Running the CDE packaged version with cde-exec is slower than running a native install (see the CDE frequently asked questions for more information) but it is a lot easier to install.