There are quite a few ‘@home’ projects out there: SETI@home, LHC@home, Einstein@home, Rosetta@home, ClimatePrediction@home (now Climate Prediction Net) – and there even used to be a Genome@home. While I’m normally worried about anything that’ll make my computer even noisier, one of the Mutable Matter volunteers got me curious about Folding@home and the wacky world of proteins. The protein world becomes even more wacky when your computer displays the graphics wrong (I can tell you…).
The Folding@home website calls proteins ‘nanomachines’ or ‘biology’s workhorses’ – they make up muscle, antibodies, enzymes etc. To carry out their tasks, proteins need to take on a particular shape. This is called ‘folding’. Sometimes, the folding goes wrong and that can have serious consequences for the organism in question. To find out more about folding and ‘mis-folding’, the Folding@home project was developed. And because it can take a protein only tens of microseconds (10,000 nanoseconds) to ‘fold’, but even the best computer in the world needs about a day to simulate a nanosecond (1/1,000,000,000 of a second), it would take 10,000 CPU days (= 30 years) to get a result (at least according to the project’s website). Hence the need for distributed computing.
What interested me was the way proteins were simulated, e.g. how they appear on your screen (yes, giant protein models appear on your screen it you electronically summon them to the foreground). I guess the first image of proteins that comes to my mind is some sort of squishy unstructured blob (probably toxic residue from biology lessons?). So how do other people imagine their proteins – or protein folding (especially as proteins can be so varied)? Do they stick with what they see on their screens? Are they hoping for some sort of protein origami to appear once the calculation is done? How do Folding@home people imagine the nanoworld?