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Many of us grew up building ship and airplane models from plastic kits. Modeling today has taken on a whole new meaning. Thanks to computers, modeling has become a vital tool in drug discovery.

At New York's Stony Brook University—about 55 miles east of Manhattan on the north side of Long Island—researchers are using 3D modeling in an effort to identify small molecules that can be used as anti-cancer agents or as antiviral inhibitors for HIV, influenza and SARS, among other diseases.

The method is called computational drug design (often called structure-based or rational design). A computer is used to model how drugs interact with their targets—usually proteins. It's done at the molecular level in 3D. Imaging is used in two ways: to help set up models and for data analysis.

"With the computational aspect, you can gain an understanding of the interactions which occur between drugs thereby enabling the design of more potent compounds," explains Robert Rizzo, Ph.D., Assistant Professor, Department of Applied Mathematics and Statistics at Stony Brook. Modeling starts with experimental structural data of the desired drug target protein. "Every atom in the protein has a point in space, whether it's carbon, nitrogen, oxygen, etc., Structures from X-ray crystallography [the science of determining the arrangement of atoms using X-rays scattered from electrons] serve as starting points for the simulations."

The Rizzo team obtains proteins from the Protein Data Bank, a public repository for 3D structural data of proteins.