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Table 1 Methods and their properties available in MODENA. Method names are mainly taken from those of corresponding structure prediction methods

From: Multi-objective optimization for RNA design with multiple target secondary structures

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 [43, 44]
centroidfoldc FE - [43, 44]
IPknote GCPAIR,SIM y [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 - -
  1. 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
  2. aRNAfold with option -p
  3. bWe use [34] for the findpath.c [24] in the Vienna RNA package
  4. cThe secondary structure of all nucleotide positions is constrained to obtain the free energy of a specified secondary structure like RNAeval
  5. dFree energy value output by CentroidFold
  6. eThe methods which can deal with pseudoknots