Glowing green/red proteins.

[susato]

The Earthlink link is dead, but the NYT article on green fluorescent protein and the Nobel prizes awarded for its discovery, is still there.

So far there's not much of a link between GFP and F@H. GFP is used as a "marker protein" by inserting it in the DNA of an organism right next to a protein that one is interested in looking at, but which is difficult to measure on its own. When the organism makes the protein of interest, it makes GFP at the same time, and the GFP is easily detected by shining light on it and watching for it to glow green. (Or blue, or red, or any of the other colors now available from mutant GFPs)

If there were some interest in how GFP folds, when in the folding process its fluorescence begins to show up, or details of the specific chemical structures and free energy levels associated with fluorescence, F@H might be a good way to answer those questions. For now, it's enough for most biotech researchers to know that GFP works reliably, is generally non-toxic to the organism it's put into, and is easy to use as a marker. Maybe in future there could be some kind of project on design of protein/small-molecule interactions, in which the protein's fluorescence would give information about its binding to the small molecule. One of the most interesting aspects of F@H is the opportunity to test F@H predictions against real biochemistry experiments. Since GFP helps make protein chemistry visible and easy to monitor, it might be a good candidate for an "in vivo"/"in vitro"/"in silico" comparison.

For example something like this.

[codysluder]

One of the most interesting aspects of F@H is the opportunity to test F@H predictions against real biochemistry experiments. Since GFP helps make protein chemistry visible and easy to monitor, it might be a good candidate for an "in vivo"/"in vitro"/"in silico" comparison.

I've tried reading the technical papers published by the Pande Group and most of the are too scholarly for me. The ones that I've read seem to be mostly in silico results but I'm not sure that my sample is representative. What percent of the results have been confirmed by an in vivo/in vitro/in silico comparison?