ProKware: integrated software for presenting protein structural properties in protein tertiary structures

Protein tertiary structure plays an essential role in deciphering protein functions, especially protein structural properties, including domains, active sites and post-translational modifications. These properties typically yield useful clues for understanding protein functions. This work presents an integrated software, named ProKware, that presents protein structural properties in protein tertiary structures, such as domains, functional sites, families, active sites, binding sites, post-translational modifications and domain–domain interaction. Using this web-based and Windows-based interface, users can manipulate and visualize three-dimensional protein structures, as well as the supported structural properties that are curated in the protein knowledge database. ProKware is an effective and convenient solution for investigating protein functions and structural relationships. This software can be accessed on the internet at

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

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: [email protected]