DESIGNING DRUGS TO ACHIEVE maximum effectiveness requires a detailed understanding of their molecular structure. But determining the structure of molecules with more than 400 atoms used to be impossible without a chemist's help, even on supercomputers. In 1992, researchers in Buffalo, N.Y., devised a method called SnB, or "shake and bake," which used a supercomputer to dope out the structure of a 414-atom molecule. Now, Russ Miller, a computer scientist at the State University of New York at Buffalo, has optimized the program to run on computer workstations costing about $4,000.
The software figures out molecular structures using data generated by bombarding a crystal of the material with X-rays and analyzing the reflections. First, the program plots a random configuration of atoms and moves them around until they fall into a configuration that more closely matches the reflection data. Then it repeats the process from a new random point, eventually selecting the best match. Molecular Structure Corp. in Houston has built the program into its existing molecular-design software.