Based on the famous ""mfold"", the UNAFold software package is an integrated collection of programs that simulate nucleic acid folding and hybridization, and its melting pathways for one or two single-stranded molecules. The package predicts folding for single-stranded RNA or DNA through combination of free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms, as well as on Mac OS X. A limited version is available for Windows; XP and Vista, although it is not recommended. Images of secondary structures, hybridizations, and dot plots can be computed using common formats. Similarly, a variety of theoretically melting profile plots can be created or imported from real experimental results. The package is ""command line"" driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. Version 4 of UNAFold allows the prediction of intra-molecular base pairs in duplexes, which should be of particular use for biotechnology applications. This newer version also works for computing partition functions of circular molecules, as significant advance. Nucleic acids calculations used for hybridizations and amplifications in: · Life science research · Drug development and discovery · Diagnostics
Features: Contains a unique ad hoc rule to correct for internal-free energy changes in unfolded, single-stranded molecules caused by base stacking. The two interacting molecules are not required to be perfectly complementary or to be related at all. User is not expected to provide hybridization; UNAFold computes minimal energies and partition functions over all possible hybridizations. Entire melting profiles are computed as a function of temperature. Allow for changes in mono-, and divalent cation concentrations. The concentration of each complementary strand do not have to be the same allowing molecular beacon simulation versus target interactions. Provides many applications in one package in an easy, user friendly manner.