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Project TitleSummer research intern on biomolecular simulation
SummaryThe intern will use molecular dynamics simulations to predict and understand binding free energies of inhibitors (drugs) to HIV protease, a key enzyme in the viral replication cycle, and drug-resistance mutants of the protease. Also perform structural studies of HIV protease mutants.
Job DescriptionThis is a position working in the laboratory of Dr. David Mobley at the University of New Orleans. The successful applicant will run molecular dynamics simulations of HIV protease, using the gromacs simulations package, and conduct binding free energy calculations using this package and internal free energy toolkits. Scripting and analysis is done using Python; knowledge of (or ability to quickly learn) Python, Matplotlib, Numpy, GROMACS, molecular dynamics, and basic Linux operations is necessary.

HIV protease is a target of many current anti-HIV drugs. However, viral drug resistance is a growing problem. Here, we seek to help understand drug resistance mutants by (a) computing binding affinities from computational methods to compare with experiment and test our methods, and (b) provide a structural and mechanistic explanation of the key energetic contributions to drug resistance. This work will help guide future drug discovery efforts.

This project builds on work that has already been done in the lab with some initial exploratory simulations on HIV protease. The successful applicant needs to be able to pick up the work that has already been done and carry it forward. Some knowledge of molecular dynamics simulations and preferably of GROMACS, Python, and the other aspects mentioned above is essential.
Conditions/QualificationsMust have molecular dynamics (GROMACS) experience, Python coding experience, experience with Matplotlib and Numpy.
Start Date05/31/2010
End Date08/13/2010
LocationDavid Mobley research group
Department of Chemistry
University of New Orleans
2000 Lakeshore Drive
New Orleans, LA 70148
Christopher Savoie