Using Stream Computing on Mainstream PC Graphics Hardware for Fast de novo Protein Structure Prediction

大多数基因被设计为编码在体内具有有用功能的特定蛋白质。蛋白质本质上是由称为氨基酸的简单分子组成的字符串，一旦蛋白质由细胞中的蛋白质制造机器（核糖体）形成，这些字符串就可以自组装成复杂的3-D结构。正是这种独特的结构决定了蛋白质的精确化学功能（即在细胞中做什么以及如何做）。通过向结晶蛋白质发射X射线，科学家可以确定它们的结构，但这一过程可能需要数月甚至数年。由于有数十万种蛋白质的天然结构是未知的，因此科学家们想要找到一种聪明的捷径来确定蛋白质的结构也就不足为奇了。我们，像许多其他科学家一样，一直在试图“破解”蛋白质结构的密码，即制定出控制蛋白质如何找到其独特结构的规则，然后试图用这些规则对计算机进行编程，以使科学家能够快速“预测”他们感兴趣的蛋白质的结构。在UCL，我们已经开创了许多从氨基酸序列预测蛋白质结构的方法。其中最成功的一种是用其他蛋白质的小片段组装新的蛋白质结构--有点像用乐高（TM）零件建造模型。虽然我们已经展示了一些成功的尝试来预测蛋白质结构，但由于需要大量的计算机能力来进行计算，因此该技术并不容易为实验室科学家所用。一个有趣的新发展，可能允许任何科学家在他自己的台式PC上运行这些蛋白质折叠模拟是使用图形芯片运行模拟的速度比PC本身快很多倍。通常，图形芯片允许用户以非常高的速度运行3D游戏或可视化3D环境，但最近很明显，这些芯片能够做的不仅仅是绘制3D对象。我们的计算表明，最新的3D图形板可在商业街不到300磅能够做尽可能多的工作，作为30个正常的个人电脑。如果实验成功，任何拥有廉价PC和显卡的科学家都可以运行我们的软件，而无需访问昂贵的超级计算机集群。

Most genes are designed to code for specific proteins which have useful functions in the body. Proteins are essentially strings of simpler molecules, called amino acids and these strings can self-assemble into a complex 3-D structure as soon as the protein is formed by the protein-making machinery (ribosomes) in the cell. It is this unique structure which determines the precise chemical function of the protein (i.e. what is does in the cell and how it does it). By firing X-rays at crystallised proteins, scientists can determine their structure, but this process can take many months or even years. With hundreds of thousands of proteins for which the native structure is unknown, it is not surprising that scientists want to find a clever shortcut to working out the structure of proteins. We, like many other scientists have been trying to 'crack the code' of protein structure i.e. working out the rules which govern how the protein finds its unique structure and then trying to program a computer with these rules to allow scientists to quickly 'predict' what the structure of their protein of interest might be. At UCL we have been pioneering a number of approaches to predicting the structure of a protein from amino acid sequence. One of the most successful assembles new protein structures from small pieces of other proteins - a little bit like building a model from Lego(TM) parts. Although we have demonstrated a number of successful attempts at predicting protein structure, the technology is not readily available to bench scientists due to the fact that a lot of computer power is needed to carry out the calculations. One interesting new development that may allow any scientist to run these protein folding simulations on his own desktop PC is the use of graphics chips to run the simulations many times faster than the PC can on its own. Normally graphics chips allow users to run 3-D games or visualise 3-D environments at very high speed, but recently it has become apparent that these chips are capable of doing a lot more than just drawing 3-D objects. Our calculations indicate that the latest 3-D graphics boards available in the high street for less than 300 pounds are able to do as much work as 30 normal PCs. If this experiment is successful, any scientist with a cheap PC and graphics card will be able to run our software without needing access to an expensive supercomputer cluster.