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                       BIOINFORMATICS COLLOQUIUM
                    School of Computational Sciences
                        George Mason University
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   RNA Conformational/Functional Variation: Prediction and Analysis

                         Bruce Shapiro, Ph.D.
                      National Cancer Institute
                    National Institutes of Health

                      Tuesday, September 28, 2004
                                4:30 pm
               Verizon Auditorium, Prince William Campus

The functional importance of RNA conformational variations is just
beginning to be characterized. Studies indicate that RNA may enter
intermediate and multiple conformational states that are key to its
functionality.  These states may have a significant impact on gene
expression and molecular function. It is known that the biologically
functional states of RNA molecules may not correspond to their minimum
energy state, that kinetic barriers may exist that trap the molecule in
a local minimum, that folding often occurs during transcription, and
that cases exist in which a molecule will transition between one or more
functional conformations.  Thus, methods for simulating the folding
pathways and dynamic behavior of an RNA molecule are important for the
prediction of RNA structure and its associated function.

This talk will concentrate on the computational techniques that we have
developed and use for the prediction and analysis of RNA structures. In
particular, we have developed a massively parallel genetic algorithm
that captures the secondary structure of intermediate and final
functional states of RNA molecules and gives significant insights into
the folding pathways associated with various RNA sequences. In addition,
we have developed data mining tools (visual and otherwise) associated
with STRUCTURELAB, our RNA structure analysis workbench, which aids in
the analysis of the massive amounts of data produced by the genetic
algorithm.

Representative examples illustrating data visualization of pathway
dynamics and conformational switching resulting from data generated by
the genetic algorithm will be discussed. In addition, since atomic level
three-dimensional simulations can provide additional critical
information on structural changes and dynamics of RNA, which is not
accessible, by any other methods, some examples of modeling and
molecular dynamics of RNA molecules will be shown.

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Refreshments are served at 4:00 pm.  Find the schedule and directions at
http://www.binf.gmu.edu/colloq.html