Brian Chen: Solving a combinatorial quandary

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CSE professor Brian Chen (left) will test his novel software in collaboration with neuroscience professor Juile Miwa, who studies the interaction between lynx proteins and nicotinic acetylcholine receptors in the brain. Photo by Christa Neu

Why do certain proteins in the body bind with some substances, but not with others?

The answer could be the difference between a drug working or not. The answer, however, is elusive by virtue of the sheer scope of mutations that make proteins vary between each other, and between individuals.

"Amino acids are the building blocks of proteins, and my copy of a protein might have just one that is different than yours," says Brian Chen, an associate professor of computer science and engineering at Lehigh University's P.C. Rossin College of Engineering and Applied Science. "But there are many different ways that one amino acid may change, and there are many different amino acids that may potentially change. So the natural question is, why don’t you test all the possibilities? Well, that would be a combinatorial nightmare. There are just too many possibilities to test in a wet lab, too many possibilities for a human to simulate on a computer, and too many possibilities for a person to keep straight in their head and consider in a systematic way."

Currently, researchers must review the data and do their best to interpret whether or not proteins are interacting, and how.

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