Listed below are links to our collaborators' pages as well as some of the software used extensively in our lab.

Folding@Home logo


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.

CSIRO logo


CSIRO (Commonwealth Scientific and Industrial Research Organization) is a large national laboratory in Australia with 13 divisions spread across more than 50 sites. Our collaborators are Tom Peat in the Division of Materials Science and Engineering, Janet Newman at the Collaborative Crystallisation Centre, as well as John Oakeshott in the Division of Ecosystem Sciences.

Gromacs logo


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.

Ocker logo


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.

OpenMM logo


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.

Rosetta logo


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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