Advances in Bioinformatics / 2016 / Article / Alg 2

Research Article

Multiphase Simulated Annealing Based on Boltzmann and Bose-Einstein Distribution Applied to Protein Folding Problem

Algorithm 2

Pseudocode SA applied to protein folding problem.
(1) Tune initial temperature () by analytical method
(2) Tune final temperature () by analytical method
(3) Setting cooling factor ()
(4)  is created by modifying the internal angles of protein
(5) 
(6) Calculate energy of protein applying a Force Field
(7) 
(8) While () do //Temperature Cycle
(9)  While (stop condition) //Metropolis Cycle
(10)   Create new solution () by modifying internal angles of the protein
(11)     Calculate Energy of proteins using a force field funtion
(12)     Obtain difference of energies between these two proteins
(13)   If (difference ≤ 0) then
(14)    
(15)    If energy() > energy() then
(16)     
(17)    end if
(18)   else
(19)   Boltzmann Probability =
(20)   If (Boltzmann Probability > random(0, 1)) then
(21)     
(22)    end if
(23)   end if
(24)  end while
(25)  Decrease by cooling function ()
(26) end while
(27) Show the best solution of PFP ()

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