A New Global Optimization Strategy for the Molecular Replacement Problem from X-ray Crystallography
Diane Jamrog
Lincoln Laboratory,
Massachusetts Institute of Technology
Tuesday, May 27, 2003 15:00-16:00,
Room 145, NIST North (820)
Gaithersburg
Tuesday, May 27, 2003 13:00-14:00,
Room 4511
Boulder
Abstract:
Knowledge of protein structures is extremely useful for medical
research, including rational drug design.
A primary technique for determining the three-dimensional
structure of a protein molecule is X-ray crystallography, in which the
molecular replacement (MR) problem often arises as a critical step.
I will present a new global optimization strategy to solve the MR
problem, a global optimization problem to
position a model protein so that it produces
calculated intensities closest to that observed from an
X-ray crystallography experiment.
The new strategy, which consists of a coarse six-dimensional
search of a surrogate function and multi-start local optimization, has
been implemented in a MR program called SOMoRe.
I will also review the performance of SOMoRe on a set of test problems,
including three problems that could
not be directly solved by traditional MR programs.
In general, improved MR methods are needed because traditional
methods, though often successful, have difficulty solving certain
classes of MR problems.
Speaker Bio:
Diane Jamrog was born and raised in Western Massachusetts.
She attended Smith College in Northampton, MA and received a B.A. in
Mathematics in 1993.
In 1996, she began attending graduate school at Rice University and
received a Master's degree in Computational and Applied Mathematics in
2001. She was a fellow of the W.M. Keck Center for Computational
Biology from 1998-2002. Working under the advisement of Yin Zhang and
Richard Tapia from the department of Computational and Applied
mathematics, as well as, George N. Phillips, Jr. from the department of
biochemistry, she completed her interdisciplinary PhD research in May
2002. She held a short postdoc at Rice University to complete work on
software that was developed during her PhD research. Currently, she is
a technical staff member at MIT Lincoln Laboratory in the Advanced
Systems Concept group.
Contact: A. J. KearsleyNote: Visitors from outside NIST must contact
Robin Bickel; (301) 975-3668;
at least 24 hours in advance.
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