The New York Times reports that a

privately financed team of scientists and engineers is nearing completion of a special-purpose supercomputer intended to offer more than a thousandfold increase in performance for complex molecular simulations.

The machine, named Anton, in homage to Anton van Leeuwenhoek, a pioneer in microbiology, is a bold gamble to jump ahead of the most powerful general-purpose supercomputers by as much as a half decade.

It could be used to investigate problems of great scientific interest, like the folding of protein molecules, and in the design of drugs based on the simulated biological activity of different molecules....

Experimentation in the use of supercomputers to model molecular interactions has been going on for more than a decade, but the field is still largely in its infancy. Simulations of processes like the folding of proteins into three-dimensional structures or the interactions between proteins or between a protein and a drug molecule hold out the promise of advancing science and drug development.

However, each simulation must be validated by experimental scientists in a laboratory setting. Thus one of the principal advantages of increased speed in simulations that now take thousands of hours on the fastest supercomputers is to speed the time to the laboratory.

Scientists said the real value of Anton might not be known until they find out what the machine can do. “Only after Anton van Leeuwenhoek used his microscope did he see protozoa in the pond water,” said Roger Brent, director of the Molecular Sciences Institute, an independent research laboratory in Berkeley, Calif.

The new supercomputer is distinguished from other molecular dynamics computing tools like I.B.M.’s BlueGene/L supercomputer and the Stanford Folding@home distributed computing project in that the machine is designed to simulate a very narrow set of problems on biological processes that take place over a millisecond or longer. Molecular simulations are now done as a series of tiny intervals that may be as short as a femtosecond, one billionth of one millionth of a second, and may last no longer than a microsecond, or one millionth of a second.

The other notable thing about the project is that it "is being led by David E. Shaw, a billionaire computer scientist. In the 1990s, Mr. Shaw was one of the most successful of an elite group of technologists pursuing computer-based trading strategies on Wall Street."