2005, Vol. 33, Web Server issue | Nicholas R. Markham and Michael Zuker
The DINAMelt web server, developed by Nicholas R. Markham and Michael Zuker, simulates the melting of one or two single-stranded nucleic acids in solution. It predicts not only the melting temperature but also the entire equilibrium melting profile as a function of temperature. The server considers various molecular species, including heterodimers, homodimers, and single-stranded molecules, and calculates their free energies, enthalpies, entropies, and heat capacities. It also simulates UV absorbance at 260 nm using published extinction coefficients and base pair probabilities. The server is more general than existing methods, allowing for non-complementary strands, unequal strand concentrations, and competition between folding and dimerization. The output includes concentration plots, heat capacity plots, absorbance plots, and thermodynamic data files. The server is connected to ongoing research and will evolve with new theories and software. The URL for the server is http://www.bioinfo.rpi.edu/applications/hybrid/.The DINAMelt web server, developed by Nicholas R. Markham and Michael Zuker, simulates the melting of one or two single-stranded nucleic acids in solution. It predicts not only the melting temperature but also the entire equilibrium melting profile as a function of temperature. The server considers various molecular species, including heterodimers, homodimers, and single-stranded molecules, and calculates their free energies, enthalpies, entropies, and heat capacities. It also simulates UV absorbance at 260 nm using published extinction coefficients and base pair probabilities. The server is more general than existing methods, allowing for non-complementary strands, unequal strand concentrations, and competition between folding and dimerization. The output includes concentration plots, heat capacity plots, absorbance plots, and thermodynamic data files. The server is connected to ongoing research and will evolve with new theories and software. The URL for the server is http://www.bioinfo.rpi.edu/applications/hybrid/.