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Protein Interaction Browser

Thu, 2003-08-07 23:27 — alf

I've put an early version of a tool for visualising networks of protein interactions online.
You'll notice that the databases are also still in their early stages. It'll be interesting to see whether they turn out to show dense clusters of interacting proteins, or a more distributed network - this may also depend on the criteria used to judge an 'interaction'. It's also interesting to see the result of the force distribution algorithm used by TouchGraph, which separates the parts of the network into roughly the same shape as a cell - the intercellular receptors on the outside, transcription factors in the centre, and intracellular signalling molecules inbetween.
Any suggestions for integrating the various databases will be most welcome.


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Fri, 2003-09-05 18:04 — oliver

user interaction

Hi Alf,

is there a posibility to learn more about your protein browser? From the pictures one can not see what user interactions are possible. Is there a source for exectuables / source code somewhere?

Best,

Oliver


Sun, 2003-08-10 03:33 — PedroBeltrao

Protein interactions

I will probably be looking at protein interactions during my work. I want to put together some already published methods on predicting protein interactions from diverse data (literature, expression profiles, sequence, structure). The next step would be to present the data in a graphical way so that the user can decide from the information what he/she is interested in and publish the data to a database. Other interesting things to do would be to get automatic datamining on the interaction partners and type of interaction (phosphorylation, ubiquitination, assembly. etc).

Are you thinking of doing any thing like this ?


Mon, 2003-08-11 18:35 — alf

Protein interactions

Not personally, no, I'm just making the graphs. There's lots of literature around at the moment though - I put a few up here yesterday. I guess you've already trawled through BIND, MIPS and the rest...