IBM said Monday it will build a computer called Blue Gene to solve the mysteries of how proteins, the workhorse molecules and building blocks of the body, get their shape. Stan Burt, a researcher in computational biology at the National Cancer Institute in Fredrick, Md., said the problem of analyzing proteins is ''one of the Holy Grails of biology.'' ''Many diseases can be traced back to problems involving proteins,'' he said, naming high blood pressure and the common cold as examples. Knowing the structure of the proteins involved could allow scientist to tailor drugs to lock on to the proteins and block them, or change their function, he said.
Proteins are strings that fold into complex shapes.
The shape largely determines how the protein works in the body, whether it transports oxygen in the blood, like hemoglobin, or breaks up molecules of fat to digest food. The problem for scientists is that the way a protein goes from a string to a functional shape is very complicated. Proteins fold in a fraction of second in the human body, yet IBM estimates that even Blue Gene will take a year to compute the folding process for a single protein with 300 links in the chain. With this many parts, the computer has to be able to ''heal'' itself by detecting failing components, sealing them off, and directing the work elsewhere. The system software is going to be very tough,'' he said.