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

BMC Bioinformatics

Table 1 Energy parameters

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

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.

ISSN: 1471-2105