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Innovating Drugs With Computer Algorithms

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Drug discovery and innovation is the focus of a team of computational biologists in the College of Engineering and Applied Science ’s Department of Applied Mathematics and Statistics who are pioneering the use of computer algorithms to treat and fight disease.

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Dima Kozakov

Their research targets artificial molecules that act by blocking the harmful effect of some protein that was created by a microbe or a malfunctioning human cell.  These dangerous proteins have binding sites that attach to molecules on the surface of cells or in other ways cause harm.

Dima Kozakov has developed computational procedures that use experimental data about the structure of these proteins to predict binding sites and then look for places on the protein surface where small designer molecules are most likely to be able to attach and disable the protein’s activity.  His work puts Stony Brook at the forefront of computational structural biology, a field that seeks to understand and predict how molecules recognize the partner molecules to which they bind.

Many protein-protein and protein-ligand complexes that certain regions of the binding surface, called hot spots, contribute disproportionately to the binding free energy. Based on this observation, Kozakov and his team of researchers have developed the protein mapping algorithm FTMAP for the identification of ‘hot spots.’ FTMAP places molecular probes on a protein surface to identify the most favorable binding positions. The mapping algorithm performs a global search of the entire protein surface for regions that bind a number of small organic probe molecules.

“Our highly ranked Department of Applied Mathematics and Statistics is on the forefront of advancing a full range of biological challenges facing society today, including genomic analysis and data mining, computational structural biology, structure based drug design, signaling and gene-regulatory networks and much more,” said Fotis Sotiropoulos, Dean, College of Engineering and Applied Sciences. “Dima’s transformational research in this emerging field demonstrates how we are bringing science fiction to life every day.”

“Dima is a true pioneer in developing new computational mathematics for modeling protein-protein interactions,” said Ken Dill, Director of the Laufer Center for Physical and Quantitative Biology at Stony Brook University and a member of the National Academy of Sciences.  “This is important for a future of more advanced drug discovery that will focus on whole biochemical pathways, rather than just single proteins.”

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