In these respects, leukotrienes are analogous to the more commonly known histamine, but research has shown leukotrienes to be much more powerful as asthma-causing agents. Before the advent of supercomputing and visualization techniques, medicinal chemists usually studied molecules in two dimensions. To develop leukotriene antagonists, it is important to first have a three-dimensional understanding of the leukotrienes' shapes over time, he says. We can take that molecule from the back of the envelope, do a three- dimensional simulation of its behavior, and see if it has the right shape. Working with visualization specialists William Sherman and Jeffrey Thingvold of NCSA's Visualization Group, Herron visualized more than 2 Gbytes of data resulting from the Cray's simulations.
People carry out molecular dynamics simulations all the time, but they only look at one.
Normally researchers would make three long movies, one on each molecule, but it's difficult to compare them visually that way. As the molecules vibrated, we wanted to see the different shapes they would take. The distance between a pair of atoms provides the basis for the histogram, which looks like a cloud. The shape and position of that cloud are meaningful, because they show where the molecule spends most of its time. LTC4 is something of a mystery, though.