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PDBpaint, a visualization webservice to tag protein structures with sequence annotations

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Item Type:Article
Title:PDBpaint, a visualization webservice to tag protein structures with sequence annotations
Creators Name:Fournier, D. and Andrade-Navarro, M.A.
Abstract:SUMMARY: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's three-dimensional space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEATrepeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually. Availability and Implementation: PDBpaint is accessible at http://cbdm.mdc-berlin.de/~pdbpaint. Code is available from http://sourceforge.net/projects/pdbpaint. The website was implemented in Perl, with all major browsers supported. CONTACT: david.fournier@mdc-berlin.de.
Keywords:Amino Acids, Internet, Protein Conformation, Proteins, Sequence Analysis, Software
Publisher:Oxford University Press
Page Range:2605-2606
Date:15 September 2011
Additional Information:This is a pre-copy-editing, author-produced PDF of an article accepted for publication in "Bioinformatics" following peer review. The definitive publisher-authenticated version "Bioinformatics 27(18): 2605-2606, 2011." is available online at: http://dx.doi.org/10.1093/bioinformatics/btr419
Official Publication:https://doi.org/10.1093/bioinformatics/btr419
PubMed:View item in PubMed

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