You will need the Mage
application. Your web browser needs to be configured to handle files of the
MimeType "chemical/x-kinemage" with the extension "kin" (In Netscape use the menu options Edit Preferences Navigator Applications). The command for
opening Mage should be "YourMageExecutable %s" (%1 for Windows), where YourMageExecutable is replaced
by the path to your local version of the Mage
application.
What Do Our Kinemage Similarity Representations Mean?
As described in Winn et al 2004 (Structure) we have used a similarity index
ranging from +1 to -1 to quantify the similarity in the electrostatic potential around
two E2 proteins. An index of +1 represents identical potentials, an index of -1 represents
complete opposites of potential (one protein always generates a negative potential where the other
generates a positive potential and vice-versa).
Here the data from all of our pairwise comparisons has been represented in three dimensional space
with points representing two proteins being closer together, the more similar their electrostatic potentials.
On this website we have two methods for colouring the kinemages. One method is by subgroups defined by
our phylogenetic analysis. This allows the opportunity to see the relationship between sequence
similarity and electrostatic potential similarity. The other method is to highlight proteins selected by the
user on
the MainPage using a red sphere. In both cases points in the kinemage can be switched off/on using the buttons
on the upper right side of the Mage display area. Clicking on a point will result in its ID being display
at the bottom left corner of the kinemage window.
The method for converting the N x N matrix of all against all protein electrostatic potential similarity indices
to a 3D plot is described in the MAGE TEXT box that opens when you load the
kinemage file. The accuracy of this conversion is described in the MAGE CAPTION that opens when you load the
kinemage file.
