RNAstructure is a product of the Mathews
Lab, University
of Rochester Medical Center, Department of
Biochemistry and Biophysics, with the help of many contributors.
Continued development of RNAstructure is made possible by the
support of NIH grant R01GM076485.
 AccessFold
 Bimolecular
folding of nucleic acids without intramolecular pairs allowed.
This
program uses a heuristic to determine accessibility to to
duplex
formation.
 AllSub
 Generate all suboptimal nucleic acid structures within a
small free energy increment of the lowest free energy
structure.
 bifold and bifoldsmp
 Bimolecular folding of nucleic acids with intramolecular
pairs allowed.
 bipartition and
bipartitionsmp
 Bimolecular partition function calculation of nucleic acids
without intramolecular pairs allowed.
 CircleCompare
 Compare
two structures for the same sequence, with the nucleic acid
backbone
arranged around a circle to facilitate easy comparisons.
 ct2dot
 Generate a dot bracket file from a CT file. The CT file can
be regenerated from the dot bracket file using dot2ct (below).
 CycleFold
 Predict canonical and noncanonical base pairs.
 design
 Find an RNA (or DNA) sequence that is expected to fold into
a given structure.
 dot2ct
 Generate a CT file from a dot bracket file. The dot bracket
file can be regenerated from the CT file using ct2dot (above).
 draw
 Draw
a structure (or structures) in Postscript from a CT file. This
can be
done a variety of ways: annotated, unannotated, circularized,
or a
combination of these.
 DuplexFold
 Bimolecular folding of nucleic acids without intramolecular
pairs allowed.
 dynalign_ii, dynalign,
dynalign_iismp, and dynalignsmp
 Find a secondary structure common to two sequences.
 DynalignDotPlot
 Generate a free energy dot plot from a Dynalign calculation,
exported as a Postscript file.
 EDcalculator and
EDcalculatorsmp
 Determine the Ensemble Defect of a structure (compared to
the ensemble of all possible structures).
 efn2 (Energy Function 2) and
efn2smp
 Determine the folding free energy change of a structure.
 EnergyPlot
 Generate a free energy dot plot from a folding calculation
save file, exported as a Postscript file.
 EnsembleEnergy
 Calculate the ensemble energy of structures from base pair
probabilities or sequence data.

 ETEcalculator and ETEcalculatorsmp
 Estimate the endtoend (ETE) distance of a sequence in nm.
 Fold and Foldsmp
 Predict the lowest free energy structure for a nucleic acid
sequence, as well as a set of low free energy structures.
 Foldcuda
 Predict the lowest free energy structure for a nucleic acid
sequence, in parallel using a GPU.
 MaxExpect
 Predict the maximum expected accuracy structure for a
nucleic acid sequence.
 Multifind
 Find noncoding RNAs in sequence alignments.
 multilign
 Find secondary structures common to multiple sequences (more
than two).
 NAPSS
 Use NMR data to improve the prediction of an RNA secondary
structure.
 oligoscreen and
oligoscreensmp
 Determine folding thermodynamics for a set of
oligonucleotides.
 OligoWalk
 Calculate
thermodynamic features of senseantisense hybridization and
predict
free energy changes of oligonucleotides binding to target RNA.
 orega
 (Optimize RNA Ends with a Genetic Algorithm) Use a genetic algorithm to evolve a sequence to change the endtoend distance.
partition and partitionsmp
 Predict nucleic acid base pairing probabilities using a
partition function.
 partitioncuda
 Predict nucleic acid base pairing probabilities using a
partition function in parallel using a GPU.
 PARTS
 Find
a secondary structure common to two nucleic acid sequences, a
sample of
those structures, and/or the probability of pairing for common
base
pairs.
 phmm
 Predict the probablistic alignment between two RNA
sequences.
 ProbabilityPlot
 Generate a base pairing probabilities dot plot from a
partition function save file, exported as a Postscript file.
 ProbablePair
 Predict
structures from base pair probabilities, using a threshold to
include
only pairs within a specific range of probabilities.
 ProbKnot (encompasses ThreshKnot)
 Predict a maximum expected accuracy structure, including
pseudoknots.
 ProbScan
 Calculate the probabilities of loops or helix stacks.
 refold
 Use a save file to predict a new set of suboptimal
structures.
 RemovePseudoknots
 Remove pseudoknots from an RNA structure, outputting the
most likely pseudoknotfree structure.
 Rsample
 Uses SHAPE mapping data to output a partition
function save file, which can be used to model the
structure of a sequence that populates multiple
conformations.
 scorer
 Calculate sensitivity and positive predictive value for two
structures being compared.
 ShapeKnots
 Predict a secondary structure that can contains pseudoknots,
restrained by SHAPE mapping data.
 stochastic and stochasticsmp
 Generate a representative ensemble of structures.
 SymmetryTester
 Test the required symmetries in a set of data tables.

 TurboFold
 Fold multiple sequences into their
optimal conformations, using one of three different folding
modes.


 TurboHomology
 Predict a secondary structure by homology modeling when there is an alignment of homologs with know structure.
