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Research Abstracts Online
January 2008 - March 2009

University of Minnesota Twin Cities
Medical School
Department of Laboratory Medicine and Pathology

PI: William B. Gleason, Fellow

Computational Approaches to Problems of Biomedical Significance

The goal of this research is to gain insight into protein/ligand interactions by using computer simulations and experimental methods. Current systems of interest include inhibitor complexes of the HIV protease and complexes of heparin-binding proteins with heparin. The latter include: anti-thrombin, acidic and basic fibroblast growth factors, and vascular endothelial growth factor. Also under investigation is protein kinase inhibition, particularly involving the clinically relevant molecules Irressa and Tarceva, which bind to the kinase domain of epidermal growth factor receptor and are two clinically relevant drugs used for cancer therapy.

Simulation methods being used range from static protein targets with flexible ligands to full molecular dynamics simulations involving flexible ligands, protein, and solvent. In some cases, the simple methods give good results (e.g. heparin/anti-thrombin). In other systems (e.g. the kinase inhibitors), account needs to be taken of the flexibility of the proteins.

Group Members

Leila Albers, Research Associate
To-Uyen T. Pham, Supercomputing Institute Undergraduate Intern
Sarah Meade, Undergraduate Student
Malgorzata M. Siorek, Undergraduate Student
Derek Straka, Undergraduate Student
Di Wu, Undergraduate Student
Chelsea Zhang, Undergraduate Student