ACO algorithms for the Hydrophobic Polar Protein Folding Problem version 3 (ACO-HPPFP-3) =============================================================== PARAMETERS: The following parameters NEED to be specified (no default values): parameter description -------------------------------- -seq hp sequence to be folded in lower case letters (e.g. hhhhpppphhh) -eng optimal energy (specify as a positive value) known or approximated (if not known use large enough number) -file output file Optional parameters that have default values (same default values for 2D and 3D): parameter default value description ------------------------------------------------------------- -runs 10 number of independent runs of an algorithm -tries 1000000 cut-off number for number of iterations (construction-local search-pheromone update) in each run -time 1000000 cut-off CPU time [sec] per run -ants 100 number of ants in the colony -noImprLS 10000 length of local search - number of non improving steps tolerated in each call to local search -alpha 1 weight for the pheromone information -beta 2 weight for the heuristic information -rho 0.8 pheromone persistence -noise 0.05 theta (pheromone noise) -elitist_ants 0.01 fraction of elitist ants (updating pheromone matrix, 0 <= elitist_ants <= 1) -fractLSants 0.5 fraction of ants chosen to perform local search (0 <= fractLSants <= 1) -probPrev 0.5 probability of keeping previous direction (in long-range move) ================================================================= EXAMPLES OF USAGE: folding in 2D: ./antsystem2D -seq pphpphhpphhppppphhhhhhhhhhpppppphhpphhpphpphhhhh -eng 23 -file seq1_3D -noImprLS 1000 -noise 0.05 -tries 1000000 -runs 3 -ants 100 -alpha 1 -beta 2 -rho 0.8 -elitist_ants 0.01 -fractLSants 0.5 -probPrev 0.5 -time 172800 folding in 3D: ./antsystem3D -seq hphhpphhhhphhhpphhpphphhhphphhpphhppphpppppppphh -eng 32 -file seq1_2D -noImprLS 10000 -noise 0.05 -tries 1000000 -runs 3 -ants 100 -alpha 1 -beta 2 -rho 0.8 -elitist_ants 0.01 -fractLSants 0.5 -probPrev 0.5 -time 172800 For more detailed information about the parameter settings both in 2D and 3D check the paper: An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem. Alena Shmygelska and Holger H Hoos,BMC Bioinformatics 2005, 6:30 (14 Feb 2005). ================================================================== OUTPUT: Console output produced: ACO algorithms for the Hydrophobic Polar Protein Folding Problem version 3 (ACO-HPPFP-3) run 0 run 1 run 2 ... [Algorithm display progress in terms of number of independent runs completed] ================================================================== File output produced: ACO algorithms for the Hydrophobic Polar Protein Folding Problem version 3 (ACO-HPPFP-3) Parameter-settings: max runs = 3 max iterations = 1000000 cut-off time = 172800 CPU sec optimal energy (known or approximated) = -32 number of ants = 100 length of local search - noImpr steps = 10000 alpha (pheromone weight) = 1 beta (heuristic info weight) = 2 rho (pheromone persistence) = 0.8 theta (pheromone noise) = 0.05 percent of elitist ants (updating pheromone matrix) = 1 % percent of ants chosen to perform local search = 50 % probability of keeping previous direction (in long-range move) = 0.5 HP sequence: hphhpphhhhphhhpphhpphphhhphphhpphhppphpppppppphh sequence size = 48 ============================================== run = 0; iteration = 1; CPU time = 0 sec; Lowest energy = -11; Conformation = udlrrduurrudrddudrudllurdldggrluruslsdlruldsduul; run = 0; iteration = 1; CPU time = 0 sec; Lowest energy = -13; Conformation = rudrssdruddslsllurdduurrssggruurrulsdrsdslldrddu; ... [Parameter settings are outputed; in each run for each improving energy value - Lowest energy we output: CPU time [sec] required to find this solution quality, iteration number in which this solution quality was found, and the actual conformation of a protein in terms of relative directions [s-straight; l-left; r-right; u-up; d-down; g-grounded amino acid (there is a pair of amino acids that serve as the point of reference)]. =====================================================================