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Table 1 Energy parameters

From: A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures

Name Description Value (Kcal/mol)
P s Exterior pseudoloop −1.38
  initiation penalty  
P s m Penalty for introducing pseudoknot 10.07
  inside a multiloop  
P s p Penalty for introducing pseudoknot 15.00
  inside a pseudoloop  
P b Band penalty 2.46
P u p Penalty for unpaired base 0.06
  in a pseudoloop  
P p s Penalty for closed subregion 0.96
  inside a pseudoloop  
e H (i,j) Energy of a hairpin loop closed by i.j  
e S (i,j) Energy of stacked pair closed by i.j  
e s t P (i,j) Energy of stacked pair that 0.89×e S (i,j)
  spans a band  
e i n t (i,r,r,j) Energy of a pseudoknot-free  
  internal loop  
e i n t P (i,r,r,j) Energy of internal loop 0.74×e i n t (i,r,r,j)
  that spans a band  
a Multiloop initiation penalty 3.39
b Multiloop base pair penalty 0.03
c Penalty for unpaired base 0.02
  in a multiloop  
a Penalty for introducing a multiloop 3.41
  that spans a band  
b Base pair penalty for a multiloop 0.56
  that spans a band  
c Penalty for unpaired base in a multiloop 0.12
  that spans a band  
  1. This table provides the names, description and values of the energy parameters and functions that we used in our methods. The names and definitions are the same as in our original HFold [48], and the values were updated based on the work of Andronescu et al. [36]. These parameters were derived for a temperature of 37°C and 1 M salt concentration.