Michael Zuker, professor of
mathematical sciences, develops tools for predicting the secondary
structure of RNA and DNA, mainly by using thermodynamic methods.
Much of his work has been on RNA structure, which is important
in understanding many biological processes, including translation
regulation in messenger RNA, replication of single-stranded RNA
viruses, and the function of structural RNAs and RNA/protein complexes.
His algorithms have been widely used for drug design, and work
on DNA folding has been very popular with the biotechnology community.
Recent work in his laboratory includes the development of methods
to predict folding hybridization and melting curves for two strands
of RNA or DNA, and he is developing statistically based rules
for RNA folding. His algorithms are available on this website,
which is so popular that the server registers as many as 800,000
hits a month. His papers outlining his algorithms get cited almost
every day of the year.
Nick Markham (Ph.D. 2006), a computer scientist who worked with
professor Zuker, created the UNAFold software package that both
replaces and extends mfold. It could be named mfold++.
His
DINAMelt web server, created in July 2005, is based on UNAFold.
By the end of 2005, he had recreated the Quikfold, Zipfold, Tm and
2-state hybridization servers and incorporated them into DINAMelt.
Current applications:
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