Table 1.
Methods and their properties available in MODENA. Method names are mainly taken from those of corresponding structure prediction methods
| Method | Property | Str. | Package |
|---|---|---|---|
| RNAfold | MFE,SIM | y | The Vienna RNA Package [16, 41] |
| RNAfold-pa | MFE,EFE,PB,SIM | y | The Vienna RNA Package [16, 41] |
| RNAeval | FE | - | The Vienna RNA Package [16, 41] |
| FindPathb | BAR | - | The Vienna RNA Package [16, 41] |
| Fold | MFE,SIM | y | RNAstructure [42] |
| foldc | FE | - | RNAstructure [42] |
| EnsembleEnergy | EFE | - | RNAstructure [42] |
| CentroidFold | FEd,SIM | y | www.ncRNA.org [43, 44] |
| centroidfoldc | FE | - | www.ncRNA.org [43, 44] |
| IPknote | GCPAIR,SIM | y | www.ncRNA.org [44, 45] |
| mfee | MFE,SIM | y | NUPACK [35] |
| pfunce | EFE,PF | - | NUPACK [35] |
| energye | FE | - | NUPACK [35] |
| probe | PB | - | NUPACK [35] |
| defecte | DEF,NDEF | - | NUPACK [35] |
| UNAFold | MFE,SIM | y | UNAFold [46] |
| pknotsRGe | MFE,SIM | y | RNA studio [47] |
| HotKnotse | MFE,SIM | y | RNAsoft [48] |
| GCe | CONT | - | - |
MFE: minimum free energy; SIM: structure similarity between target and predicted secondary structures [28]; EFE: ensemble free energy; PB: Boltzmann probability; FE: free energy of a specified target structure; BAR: energy barrier height between two specified target structures; GCPAIR: GC content of base paired nucleotides multiplied by -1; PF: partition function; DEF: ensemble defect; NDEF: normalized ensemble defect; CONT: GC content. The str. column indicates whether the method assigns a predicted structure to each individual or not
aRNAfold with option -p
bWe use accessFindPath.py [34] for the findpath.c [24] in the Vienna RNA package
cThe secondary structure of all nucleotide positions is constrained to obtain the free energy of a specified secondary structure like RNAeval
dFree energy value output by CentroidFold
eThe methods which can deal with pseudoknots