Pro-Origami statistics

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Number of citations per year for the bioinformatics software tool Pro-Origami
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Protocols

Pro-Origami specifications

Information


Unique identifier OMICS_13634
Name Pro-Origami
Interface Web user interface
Restrictions to use None
Input data Protein structure, PDB files, PDB or SCOP identifier
Output data Protein structure cartoons
Output format SVG, PNG
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Alex Stivala

Publication for Pro-Origami

Pro-Origami citations

 (13)
library_books

The dynamic intein landscape of eukaryotes

2018
Mob DNA
PMCID: 5784728
PMID: 29416568
DOI: 10.1186/s13100-018-0111-x

[…] ite, despite being from inteinless hosts. Each structure file was truncated to include the domain, or portion of the protein, with intein insertion. All shortened structure PDB files were uploaded to Pro-Origami software (http://munk.csse.unimelb.edu.au/pro-origami/) []. For conservation, a single full-length extein sequence was chosen as a query and uploaded to ConSurf []. An automatic multiple s […]

library_books

Leishmania infantum 5’ Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target

2017
BMC Struct Biol
PMCID: 5738077
PMID: 29258562
DOI: 10.1186/s12900-017-0079-7

[…] The secondary structures of LiMTAP, TbMTAP and huMTAP (PDBid: 1CG6) were detected using the STRIDE program [] under the Pro-origami web server ( http://munk.csse.unimelb.edu.au/pro-origami/; []). Advanced options were used to exclude 310 helices and pi helices. Topology diagrams were then generated and manually labeled […]

library_books

SAF A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin Associated RNAs

2017
Cell
PMCID: 5473940
PMID: 28622508
DOI: 10.1016/j.cell.2017.05.029

[…] ndran plot: 98.9% of residues in favored and allowed regions) and packing quality (average Z-score −1.04). PyMol (http://www.pymol.org) was used for 3D visualization, analysis and figure preparation. Pro-origami was used to create the 2-D cartoon topology schematic (). The target-template alignment was generated and annotated using EsPript v3 (). […]

library_books

Comparative visualization of protein secondary structures

2017
BMC Bioinformatics
PMCID: 5333176
PMID: 28251875
DOI: 10.1186/s12859-016-1449-z

[…] of 3D representation of the same data.According to Stivala et al. [], there are four systems specializing in automatic generation of protein structure diagrams. The main contribution of their system, Pro-origami, lies in novel approach to automatic creation of diagram layout of protein structure cartoons. This system provides diagrams which are clear, accurate, interactive, and editable. However, […]

library_books

MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode

2016
Sci Rep
PMCID: 4915002
PMID: 27324530
DOI: 10.1038/srep28226

[…] ary structures were superimposed using the CONSURF server (http://consurf.tau.ac.il/) or the Superpose program of the ccp4 suite. The folds of MtrA and MetH family proteins () were compared using the Pro-Origami server (http://munk.csse.unimelb.edu.au/pro-origami/). […]

library_books

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level

2016
BioData Min
PMCID: 4728770
PMID: 26819632
DOI: 10.1186/s13040-016-0083-7

[…] atomic coordinate data as input, locations of the elements in two-dimensional space are computed that resemble the three-dimensional topology as closely as possible. For example, TopDraw [], HERA [], Pro-origami [] and TOPS [] are tools for generating such representations. Furthermore, precomputed topology diagrams of solved structures can be found at the PDBsum database []. PROTTER [] is a recent […]


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Pro-Origami institution(s)
Department of Computer Science and Software Engineering, The University of Melbourne Parkville Campus, Victoria, Australia; Clayton School of Information Technology Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University Clayton Campus, Clayton, Victoria, Australia
Pro-Origami funding source(s)
The Australian Research Council, NICTA, ARC Federation Fellow, Honorary National Health and Medical Research Council Principal Research Fellow, Australian Postgraduate Award.

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