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Folding@Home is a large distributed computing network used for studying protein folding through molecular dynamics simulation, run by Prof. Vijay Pande at Stanford University. Donors download a "screen saver" that runs small pieces of a simulation while their computer is idle. These results are assembled by a server and analyzed to better understand the process of protein folding.
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GROMACS is an open-source molecular dynamics software package that boasts incredible computational speeds and very accurate results. We make extensive use of this software package in the Lucent Lab.
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Ocker is a docking software package written by Kim Branson and co-written by John Chodera and Del Lucent. It is used to bring together shape-based posing and a number of scoring methods to effectively identify inhibitors of protein-protein interactions.
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OpenMM is toolkit for high performance molecular simulation. In addition to having a very intuitive application layer (enabling rapid prototyping of new algorithms in python), OpenMM has ported many molecular dynamics algorithms to graphics processing units. This has been shown to give tremendous increases in computational efficiency for specific types of simulations. We are in the process of using OpenMM for the purpose of computational enzyme design.
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Rosetta is a multi-purpose molecular design software package developed by Prof. David Baker at the University of Washington and maintained by the Rosetta Commons. Rosetta has shown tremendous success in the fields of protein structure prediction, protein design, enzyme design, and structure refinement. In the Lucent Lab, we are interested in using Rosetta for enzyme design.
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