David Fournier1, Miguel A Andrade-Navarro. 1. Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. david.fournier@mdc-berlin.de
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.
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.
Authors: David Fournier; Gareth A Palidwor; Sergey Shcherbinin; Angelika Szengel; Martin H Schaefer; Carol Perez-Iratxeta; Miguel A Andrade-Navarro Journal: PLoS One Date: 2013-11-21 Impact factor: 3.240