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Variants_on_protein

Summary Table

NAME CITATION YEAR
DOG Ren J, Wen L, Gao X, Jin C, ...&, Yao X. (2009) DOG 1.0: illustrator of protein domain structures Cell Res., 19 (2) 271-273. doi:10.1038/cr.2009.6. PMID 19153597 2009
IBS Liu W, Xie Y, Ma J, Luo X, ...&, Ren J. (2015) IBS: an illustrator for the presentation and visualization of biological sequences Bioinformatics, 31 (20) 3359-3361. doi:10.1093/bioinformatics/btv362. PMID 26069263 2015
MuPIT Niknafs N, Kim D, Kim R, Diekhans M, ...&, Karchin R. (2013) MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures Hum. Genet., 132 (11) 1235-1243. doi:10.1007/s00439-013-1325-0. PMID 23793516 2013
Protter Omasits U, Ahrens CH, Müller S, Wollscheid B. (2014) Protter: interactive protein feature visualization and integration with experimental proteomic data Bioinformatics, 30 (6) 884-886. doi:10.1093/bioinformatics/btt607. PMID 24162465 2014

DOG

  • NAME : DOG
  • SHORT NAME : DOG
  • FULL NAME : Domain Graph
  • DESCRIPTION : a novel software of DOG for experimentalists, to prepare publication-quality figures of protein domain structures
  • URL : https://dog.biocuckoo.org/
  • TITLE : DOG 1.0: illustrator of protein domain structures
  • DOI : 10.1038/cr.2009.6
  • CITATION : Ren J, Wen L, Gao X, Jin C, ...&, Yao X. (2009) DOG 1.0: illustrator of protein domain structures Cell Res., 19 (2) 271-273. doi:10.1038/cr.2009.6. PMID 19153597
  • JOURNAL_INFO : Cell research ; Cell Res. ; 2009 ; 19 ; 2 ; 271-273
  • PUBMED_LINK : 19153597

IBS

  • NAME : IBS
  • SHORT NAME : IBS
  • FULL NAME : illustrator of biological sequences
  • DESCRIPTION : an illustrator for the presentation and visualization of biological sequences
  • URL : http://ibs.biocuckoo.org/
  • TITLE : IBS: an illustrator for the presentation and visualization of biological sequences
  • DOI : 10.1093/bioinformatics/btv362
  • ABSTRACT : UNLABELLED: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. AVAILABILITY AND IMPLEMENTATION: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. CONTACT: renjian.sysu@gmail.com or xueyu@hust.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  • COPYRIGHT : http://creativecommons.org/licenses/by-nc/4.0/
  • CITATION : Liu W, Xie Y, Ma J, Luo X, ...&, Ren J. (2015) IBS: an illustrator for the presentation and visualization of biological sequences Bioinformatics, 31 (20) 3359-3361. doi:10.1093/bioinformatics/btv362. PMID 26069263
  • JOURNAL_INFO : Bioinformatics (Oxford, England) ; Bioinformatics ; 2015 ; 31 ; 20 ; 3359-3361
  • PUBMED_LINK : 26069263

MuPIT

  • NAME : MuPIT
  • SHORT NAME : MuPIT
  • FULL NAME : Mutation position imaging toolbox
  • DESCRIPTION : Webserver for mapping variant positions to annotated, interactive 3D structures
  • URL : http://mupit.icm.jhu.edu/MuPIT_Interactive/
  • TITLE : MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures
  • DOI : 10.1007/s00439-013-1325-0
  • ABSTRACT : Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the exome sequencing project. MuPIT interactive is freely available for non-profit use at http://mupit.icm.jhu.edu .
  • CITATION : Niknafs N, Kim D, Kim R, Diekhans M, ...&, Karchin R. (2013) MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures Hum. Genet., 132 (11) 1235-1243. doi:10.1007/s00439-013-1325-0. PMID 23793516
  • JOURNAL_INFO : Human genetics ; Hum. Genet. ; 2013 ; 132 ; 11 ; 1235-1243
  • PUBMED_LINK : 23793516

Protter

  • NAME : Protter
  • SHORT NAME : Protter
  • FULL NAME : Protter
  • DESCRIPTION : interactive protein feature visualization and integration with experimental proteomic data
  • URL : https://wlab.ethz.ch/protter/start/
  • TITLE : Protter: interactive protein feature visualization and integration with experimental proteomic data
  • DOI : 10.1093/bioinformatics/btt607
  • ABSTRACT : SUMMARY: The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Here we present Protter, a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins. A built-in export function produces publication-quality customized protein illustrations, also for large datasets. Visualizations of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics. AVAILABILITY AND IMPLEMENTATION: The Protter web application is available at http://wlab.ethz.ch/protter. Source code and installation instructions are available at http://ulo.github.io/Protter/. CONTACT: wbernd@ethz.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  • CITATION : Omasits U, Ahrens CH, Müller S, Wollscheid B. (2014) Protter: interactive protein feature visualization and integration with experimental proteomic data Bioinformatics, 30 (6) 884-886. doi:10.1093/bioinformatics/btt607. PMID 24162465
  • JOURNAL_INFO : Bioinformatics (Oxford, England) ; Bioinformatics ; 2014 ; 30 ; 6 ; 884-886
  • PUBMED_LINK : 24162465