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Image showing the interaction of
the binding module (CBM) of Cellobiohydrolase I after
2.5 and 7.5ns of molecular dynamics simulation. It can
be seen that a tyrosine residue (shown in
red)
unfolds and interacts directly with the cellulose
surface indicating a possible induced fit mechanism.
Such simulations are an integral part of DoE efforts to
develop next generation enzymes for cellulose to
bioethanol conversion. This research, conducted in
collaboration with the
National
Renewable Energy Laboratory is
described in PEDS 2007 p179 (Image by Ross Walker & Amit
Chourasia [SDSC]) |
What we do...
The research focus of the
Walker Molecular Dynamics (http://www.wmd-lab.org),
based at the San Diego Supercomputer
Center at the University of California San Diego, encompasses the
fields of computational chemistry, molecular biology and high
performance computing. The lab is particularly interested in the
development of efficient algorithms for parallel computation of
Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM)
techniques as well as improvements in the computational efficiency
and accuracy
of classical MM dynamics simulations. The research also focuses on
the use of MM and QM/MM Molecular Dynamics algorithms for the
determination of physical and chemical properties of protein based
systems.
The
lab is funded through a combination of grants from the U.S.
Department of Energy (DOE), the National Science Foundation (NSF)
and the University of California. Practical applications of the
techniques developed in the lab include the development of next
generation viral inhibitors and improvement of the efficiency of
cellulose to bio-ethanol conversion in support of the U.S. DoE
mandate to replace the use of fossil fuels with clean renewable
sources.
The lab is also closely involved with the
development of the
AMBER
molecular dynamics software.
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