PDBpaint, a visualization webservice to tag protein structures with sequence annotations
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- David Fournier
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000294755400019&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/bioinformatics/btr419
- eISSN
- 1367-4811
- Externe Identifier
- Clarivate Analytics Document Solution ID: 818MI
- PubMed Identifier: 21757464
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 18
- Zeitschrift
- BIOINFORMATICS
- Paginierung
- 2605 - 2606
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Titel
- PDBpaint, a visualization webservice to tag protein structures with sequence annotations
- Sub types
- Article
- Ausgabe der Zeitschrift
- 27
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Abstract
- <jats:title>Abstract</jats:title> <jats:p>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 3D 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 HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually.</jats:p> <jats:p>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.</jats:p> <jats:p>Contact: david.fournier@mdc-berlin.de</jats:p>
- Autoren
- David Fournier
- Miguel A Andrade-Navarro
- DOI
- 10.1093/bioinformatics/btr419
- eISSN
- 1367-4811
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 18
- Zeitschrift
- Bioinformatics
- Sprache
- en
- Online publication date
- 2011
- Paginierung
- 2605 - 2606
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/bioinformatics/btr419
- Datum der Datenerfassung
- 2023
- Titel
- PDBpaint, a visualization webservice to tag protein structures with sequence annotations
- Ausgabe der Zeitschrift
- 27
Datenquelle: Crossref
- Abstract
- <h4>Summary</h4>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 3D 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 HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually.<h4>Availability and implementation</h4>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.<h4>Contact</h4>david.fournier@mdc-berlin.de.
- Addresses
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. david.fournier@mdc-berlin.de
- Autoren
- David Fournier
- Miguel A Andrade-Navarro
- DOI
- 10.1093/bioinformatics/btr419
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Identifier: 21757464
- Open access
- false
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 18
- Zeitschrift
- Bioinformatics (Oxford, England)
- Schlüsselwörter
- Amino Acids
- Proteins
- Sequence Analysis, Protein
- Protein Conformation
- Internet
- Software
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2011
- Paginierung
- 2605 - 2606
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Datum der Datenerfassung
- 2011
- Titel
- PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
- Sub types
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 27
Datenquelle: Europe PubMed Central
- 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 3D 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 HEAT-repeats), 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.
- Autoren
- David Fournier
- Miguel A Andrade-Navarro
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/21757464
- DOI
- 10.1093/bioinformatics/btr419
- eISSN
- 1367-4811
- Ausgabe der Veröffentlichung
- 18
- Zeitschrift
- Bioinformatics
- Schlüsselwörter
- Amino Acids
- Internet
- Protein Conformation
- Proteins
- Sequence Analysis, Protein
- Software
- Sprache
- eng
- Country
- England
- Paginierung
- 2605 - 2606
- PII
- btr419
- Datum der Veröffentlichung
- 2011
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2012
- Titel
- PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 27
Datenquelle: PubMed
- Beziehungen:
- Eigentum von