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Research Abstracts Online
January 2009 - March 2010

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

PI: Yuk Sham

Method in Calculating Absolute Binding Free Energies

Molecular recognition is key to cellular signaling processes and enzymatic reactions. The ability to quantify consistently and reliably the absolute binding energy for molecular binding is fundamental to enhancing our understanding of the energetic basis behind functional structural protein. It can also provide a rational model for computer-aided protein engineering and drug design that can be tested and validated with experimental observations. The main objectives of this project are: to develop a physically consistent and reliable computational approach to evaluate absolute binding energy that is consistent with experimental observations; to evaluate the effect of sequence mutation to binding; and to rationally design mutant proteins and ligands that can be synthesized and tested for binding specificity and strength as a means to validate a computational model. The group’s computational effort will focus on protein associate processes and selective ligand binding processes.

Group Members

Roshai Dahal, Undergraduate Student
Serdan Durdagi, Research Associate
Evelyn Huang, Undergraduate Student
Hiqmet Kamberaj, Research Associate
Garrett T. McLean, Undergraduate Student
Sergey Negrashov, Undergraduate Student
Jake Stricherz, Supercomputing Institute Undergraduate Intern
Zhengqiang Wang, Faculty Collaborator