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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

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

-

-

  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 accessFindPath.py [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