Chaotic Multiquenching Annealing Applied to the Protein Folding Problem

Algorithm 3

AP pseudocode.

(1)  Annealing Phase Procedure

(2) Begin

(3)  AlphaAnnealing = initial value

(4)  T = Final temperature of MQP (Threshold value)

(5)  𝑇_final = very close to zero

(6)  Beta = value calculated by analytical method

(7)  MC = initial value

(8)  Repeat //External Loop

(9)    k = 1

(10)    Repeat //Internal Loop (Metropolis Cycle)

(11)      𝑆_𝑗 = New solution (𝑆_𝑖)

(12)      DE = 𝐸(𝑆_𝑗)−𝐸(𝑆_𝑖)

(13)      If DE ≤ 0 Then

(14)         𝑆_𝑖=𝑆_𝑗

(15)      else if e ^∧(DE/T) > random [0,1] Then

(16)         𝑆_𝑖=𝑆_𝑗

(17)      end if

(18)        If 𝑆_𝑖 < 𝑆_min then

(19)         𝑆_min = 𝑆_𝑖

(20)      end if

(21)    Until k < MC

(22)    T = AlphaAnnealing * T

(23)    MC = Beta * MC

(24)    k = k + 1

(25)  Until T > 𝑇_final

(26) End procedure