Fold.it: wasting time in a good cause
I just spent the better part of a Saturday playing with Foldit. Foldit is an ongoing experiment in finding protein structures by harnessing the power of the mob – or gamers, as is the case here. The player is presented with a backbone & sidechain configuration, with the secondary structures mostly pre-determined. The problem is to get the protein to fold into the correct conformation. You can tweak the secondary structures, rubberband the beta strands together into sheets and rotate the sidechains. The residues are colored by hydrophobicity, so you know who should be facing where. The 23 tutorial cases walk you through the simple yet powerful interface to folding the structures. You can rotate helices, rubberband strands, flip sheets, etc. The interface gives you feedback on sidechain clashes and voids in the structure among other things. The examples also teach you the basic of protein structural considerations: maximize hydrogen bonds, hydrophobic side chains should be buried in the structure, strands should combine to sheets, and so on. When you feel you are ready, you can start solving the various folding puzzles presented online. You can work solo, or as part of a team. The “correct solution” is, of course, unknown. The best you can do is accumulate as many points as you can, which represent how stable is the conformation you are building. Foldit, like many other cool things in structural biology, is the product of David Baker’s lab at the University of Washington. Here is a video from the YouTube UWFoldit channel showing the coolness of it all. If you decide to get your fold on, make sure you can make the time. It’s flippin’ addictive.