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Research Abstracts Online
January - December 2011

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University of Minnesota Twin Cities
Academic Health Center
Center for Drug Design

PI: Yuk Sham

Computer Studies of Molecular Recognition Processes

Molecular recognition plays a key role in cellular signaling processes and enzymatic reactions. The ability to quantify consistently and reliably the association of free energy is fundamental to enhancing our understanding of the energetic basis governing protein functions. It can also provide a rational basis for computer-aided protein engineering and drug design that can be validated with experimental observations. 

The main objectives of this group’s research are: to develop physically consistent and reliable computational approaches to evaluate absolute binding energy that is consistent with experimental observations; to evaluate the effect of sequence mutation to binding; and to rationally design proteins and ligands for model validation. The group’s computational effort focuses on: the protein assembly processes of the chemokine, troponin, HIV integrase, beta-lactamase-beta lactamase inhibitory protein complex, and dengue envelope proteins; and the ligand binding specificity for breast cancer resistance protein, HIV protease, reverse transcriptase, integrase, histone deacylase, inosine monophosphate dehydrogenase, NAD kinase, and beta-lactamase.

Group Members

Ryan Baumgartner, Undergraduate Student
Gerry R. Boss, University of San Diego, San Diego, California
Matthew Brenner, University of California–Irvine, Irvine, California
Feng Chen, Research Associate
Daune Crankshaw, Research Associate
Roshani Dahal, Graduate Student
Ben Duckworth, Research Associate
Wilsen Hadiwikarsa, Undergraduate Student
Kenny G. Hoang, Undergraduate Student
Evelyne M. Houang, Graduate Student
Kyle Konze, Undergraduate Student
Garrett T. McLean, Staff
Herbert T. Nagasawa,
Steven E. Patterson, Faculty Collaborator
Ce Shi, Research Associate
Austin Shin, Graduate Student
Zhengqiang Wang, Research Associate
Richard L. Wood, Research Associate
Han Wool Yoon, Undergraduate Student