Table 1.

Energy parameters

Name	Description	Value (Kcal/mol)
Ps	Exterior pseudoloop	−1.38
	initiation penalty
Psm	Penalty for introducing pseudoknot	10.07
	inside a multiloop
Psp	Penalty for introducing pseudoknot	15.00
	inside a pseudoloop
Pb	Band penalty	2.46
Pup	Penalty for unpaired base	0.06
	in a pseudoloop
Pps	Penalty for closed subregion	0.96
	inside a pseudoloop
eH(i,j)	Energy of a hairpin loop closed by i.j
eS(i,j)	Energy of stacked pair closed by i.j
estP(i,j)	Energy of stacked pair that	0.89×eS(i,j)
	spans a band
eint(i,r,r′,j)	Energy of a pseudoknot-free
	internal loop
eintP(i,r,r′,j)	Energy of internal loop	0.74×eint(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.