RNAstructure is a product of the Mathews Lab, University of Rochester Medical Center, Department of Biochemistry and Biophysics.
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).
 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.
 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.
 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.
 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
 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.
 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.
 TurboFold
 Fold multiple sequences into their optimal conformations, using one of three different folding modes.
