An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-12

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>cids) in 2D (left side) and Sequence S2-6 from Table 1 (48 amino acids) in 3D. Crosses and circles represent mean values for an ensemble of 100 native structures found by ACO-HPPFP-3 and PERM, respectively

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-14

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>nimal energy conformations of Sequence S1-8 in 2D (length 64, left side) and Sequence S2-5 in 3D (length 48, right side)

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-15

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p> left side) and Sequence S2-5 in 3D (length 48, right side), as a function of ant colony size and the maximum number of non-improving local search steps

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-11

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>ino acids) in 2D (left side) and Sequence S2-6 from Table 1 (48 amino acids) in 3D. Crosses and circles represent mean values for an ensemble of 100 native structures found by ACO-HPPFP-3 and PERM, respectively

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-3

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>HPPFP-3 in an average CPU time of 1.5 hours and by PERM in = = = 78 hours

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-16

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p> left side) and Sequence S2-5 in 3D (length 48, right side), as a function of the probability of retaining previous directions () during long-range mutation moves

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-7

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>; ACO-HPPFP-3 reaches this conformation much faster than PERM when folding from the left end (mean run-time over 100 successful runs for ACO-HPPFP-3: 236 CPU seconds, compared to = 3 795, = 1, = 2 CPU seconds for PERM). Right side: Unique native conformation of another designed sequence, D-2 (length 60, energy -17); ACO-HPPFP-3 finds this conformation much faster than PERM folding from either end (mean run-time over 100 successful runs for ACO-HPPFP-3: 951 CPU seconds, compared to = 9 257, = 19 356, = 12 524 CPU seconds for PERM)

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-10

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>(B50-4, 50 amino acids) in 2D (left side) and Sequence S2-6 from Table 1 (48 amino acids) in 3D. Crosses and circles represent mean values for an ensemble of 100 native structures found by ACO-HPPFP-3 and PERM, respectively

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-2

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>al search phases of our ACO algorithm in 3D

An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem-13

<p><b>Copyright information:</b></p><p>Taken from "An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem"</p><p>BMC Bioinformatics 2005;6():30-30.</p><p>Published online 14 Feb 2005</p><p>PMCID:PMC555464.</p><p>Copyright © 2005 Shmygelska and Hoos; licensee BioMed Central Ltd.</p>rage CPU time required for obtaining minimal energy conformations of Sequence S1-8 in 2D (length 64, left side) and Sequence S2-5 in 3D (length 48, right side)