Understanding how proteins form could yield unimagined medical and scientific possibilities. But simulating protein formation requires vast resources. Computational chemist Ronald Levy develops methods for reducing the time simulations need.

If you think making a paper crane is hard, try folding up a protein.

In nature's ultimate origami, cells use information encoded in genes to construct a long chain of amino acids. The chain then compacts into a tangle of loops, helices, and sheets. A protein's unique geometry enables it to interact with other molecules and do the body's biochemical heavy lifting -- turning genes on and off during fetal development, for example, or regulating digestion. Because of its complexity, simulating protein folding and proteins' interactions with other molecules is one of the toughest problems in computational biology.

  Levy group members
From left to right:
back row - Anthony Felts, Michael Andrec, Lynne Reed Murphy, Emilio Gallicchio, Peicheng Du
front row - Linda Zhang, Anders Wallqvist, Ronald Levy, Masahito Kubo

Using NCSA's SGI Origin2000 system, computational chemist Ronald Levy and his colleagues at Rutgers University in Piscataway, NJ, are developing faster and more accurate simulations of proteins in their natural environment -- water.

These improved "solvation models" may come in handy when the Human Genome Project finishes decoding the estimated 100,000 genes in the human body. Proponents of the genome project promise that this "book of life" will revolutionize medicine and biology. But first scientists have to learn how to read it. Levy hopes that his computer models will help translate genetic code into clues about the structure and function of newly discovered proteins.

Access Online | Posted 12-14-1999

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