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Home | Core Research: Cheminformatics and Bioinformatics

Cheminformatics and Bioinformatics

Jiali Gao
George Karypis
Yiannis Kaznessis
Hans Othmer
Marc Riedel

Recent Research Highlights

Professor Yiannis Kaznessis

How do antimicrobial peptides work? Dr. Allison Langham and Professor Yiannis Kaznessis, Department of Chemical Engineering and Materials Science, simulated the pore that is formed by protegrin-1, a potent antimicrobial peptide, in the lipid bilayer membrane of bacteria. The simulations show exactly how a protegrin pore allows ions and other cell contents to leak out of the bacterion, causing its death. In the picture, the cross sectional view of a protegrin-1 pore (in green) in a lipid bilayer is shown (lipid chains in grey and lipid heads in red; water is cyan). The movement of ions through the pore was visualized using molecular dynamics simulations (in yellow, a chloride ion is shown as it moves through the pore). This information helps to elucidate the mechanism of action by which this antimicrobial peptide kills bacteria and rationalizes engineering of novel, potent antibiotic molecules. The top view of the full system is shown in the insert.

Kaznessis Group — About Us

We are interested in synthetic biology. This is an exciting discipline at the interface of biological and engineering sciences. The objective is to build new, useful biological circuits, devices and systems. In our group, we combine genetic engineering experiments and theoretical models of gene networks to design bio-logical AND gates, toggle switches and protein devices in bacteria.

We place emphasis on the development of multi-scale models for synthetic biology. We use statistical mechanics to develop multiscale models of biomolecular interactions. With these we can design computer-aided synthetic biosystems. We are making available the Synthetic Biology Software Suite, available for Windows, Mac and Linux machines (

With sophisticated simulation and optimization algorithms, we are figuring out how to teach bacteria new tricks, to respond to our signals on demand. We are also experimenting with novel gene circuits with applications in biofuels, gene therapies and biosensing.

We are also interested in the molecular aspects of protein functionality, protein-protein and protein-membrane interactions. The goal is the design of synthetic biopharmaceutical products, such as antimicrobial peptides.

Prof. Kaznessis also directs the University of Minnesota Bioinformatics Summer Institute, a summer undergraduate education program funded by the National Institutes of Health and the National Science Foundation. For more information go to

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Contact Information

Digital Technology Center

499 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455

P: (612) 624-9510

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