mfold & UNAFold
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++.
RNA & DNA Folding Applications
The RNA and DNA folding servers compute multiple foldings and dot plots for single sequences. The results include images of all computed foldings. Structures may be redrawn to produce more pleasing results.
There are currently five "bulk" servers that produce fast results for many (pairs of) sequences in a single job. Output is limited. The Nucleic Acid Quikfold server folds many sequences at once. The Zipfold server computes minimum free energies only. The Tm server computes minimum free energies together with (two-state) melting temperatures. Similarly, the 2-state hybridization server computes minimum free energies and melting temperatures for the hybridization of pairs of sequences.
Given a sequence together with a secondary structure, the "Structure display" server (also call the "Free energy determination" server) computes the free energy of the structure together with images. The user may redraw the images.