What Cube can do with your list of protein sequences, divided into families

Produce a 3D map highlighting regions of specialization in one or more protein groups for import into Pymol ...
 
... 1D specialization map in png format, suitable for import and further annotation in your favorite presentation software ... ... and a spredsheet to which you can add your own annotation.
 

Click here to see a sample results page.

Nice. What does that have to do with my research?

These are tools for planining your experiment.

Check out the regions on the surface in which the families differ. Cube indicates them in shades of orange. Typically they coincide with a position of interaction specific for the subfamily of proteins. If the structure is not known, or if the protein is disordered, we have to work with the 1D information alone. A bit more difficult, but still doable.

Collect in the spreadsheet information/annotation from all sources that you have available - including your own previous work. To start you off, Cube will provide the info about conservation, specialization, and protein surface, where available. Put it all together in a slide, against the backdrop of the conservation map, and use for discussion with your geek friends. Do you know already that one of the families engages in a particular interaction the others do not? Specialization regions are good candidates for the separation-of-function mutational analysis.

Do you know already that one of the families engages in a particular interaction the others do not? Specialization regions are good candidates for the separation-of-function mutational analysis.

Click here to see some worked examples.