INTRODUCTION

The Classification Viewer is a component designed to show the kinase classification created by the PKR team and can be used for navigation, loading entries into the viewers or finding a kinase's place in the hierarchical view of the superfamily.

The classification is based on the original clustering work done at Kinase Sequence Database. The entire kinase superfamily was clustered into approximately 300 distinct families and sequence alignments were created for all of them (reference). Each family alignment was then used to generate a consensus sequence, which were combined into a multiple sequence alignment as a subset of the master alignment of the database content. As the next step, CLUSTALW and PHYLIP packages were used to produce a phylogeny tree. The latter was then manually edited and the families were mapped to kinase groups present in the Protein Kinase Resource and compared to the human kinome classification (Manning et al.).

The resulting classification covers almost the entire content of the Protein Kinase Resource and features eight distinct classes of protein kinases. Seven of them are found in the human kinome classification, and the eighth is a class specific to plant kinases with no close relation to the other classes. At this point, a more detailed refinement is being done, and this preliminary classification is provided as a test case in order to solicit your input on the quality and possible changes in the existing tree.

The Classification Viewer uses a simple tree representation model, which dynamically reflects the content of the database. We plan to use a different graphical representation for the classification tree at the Protein Kinase Resource web site. In any event, any comments as to usability and accuracy of the viewer and the classification content will be most welcome.

If you would like to contribute any suggestions or ideas regarding the kinase clasification and the viewer, please email us.