NASP is a computer program that will allow predict the most evolutionarily conserved secondary structures evident within a set of aligned nucleic acid sequences. It will progressively identify all of the most probable secondary structures that display some degree of sequence conservation between sequences in an analysed alignment.
QRNAS (Quick Refinement of Nucleic Acid Structures) is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues.
UNAFold (Unified Nucleic Acid Folding & Hybridization Package) is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for single-stranded RNA or DNA combines 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 (C(p)), and mole fractions of different molecular species are computed as a function of temperature.
mfold has been replaced by UNAFold.Although UNAFold will install without mfold_util, the sir_graph and boxplot_ng programs from the mfold_util package are required in order to obtain structure plots and dot plots from UNAFold. Install mfold_util before installing UNAFold. Versions 3.4 and higher of mfold contains all of the non-interactive programs in mfold_util, so a separate download is not required.
Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids.Sfold is based on patent-pending algorithms developed by Ding and Lawrence (2001, 2002, 2003) for RNA folding, prediction of target accessibility, and rational design of RNA-targeting nucleic acids. The RNA folding algorithm generates a statistical sample of secondary structures from the Boltzmann ensemble of RNA secondary structures. From a statistical mechanics perspective, an RNA molecule can have a population of structures distributed according to a Boltzmann distribution, which gives the probability of a secondary structure I at equilibrium as (1/U)exp[-E(I)/RT], where E(I) is the free energy of the structure, R is the gas constant, T is the absolute temperature, and U is the partition function for all admissible secondary structures of the RNA sequence. The algorithm samples secondary structures exactly and rigorously according to the Boltzmann distribution, using recent Turner free energy rules.