Table 1 2D and 3D HP standard benchmark instances. Benchmark instances for the 2D and 3D HP Protein Folding Problem used in this study with optimal or best known energy values E*. Most instances for 2D and 3D HP can also be found in [44]; Sequence S1-9 (2D) is taken from [45], and the last two instances (2D) are from [21]. H i and P i indicate a string of i consecutive H's and P's, respectively; likewise, (s) i indicates an i-fold repetition of string s.
From: An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem
ID | Length | E* | Protein Sequence |
|---|---|---|---|
2D HP | |||
S1-1 | 20 | -9 | (HP) 2 PH 2 PHP 2 HPH 2 P 2 HPH |
S1-2 | 24 | -9 | H2(P2H)7H |
S1-3 | 25 | -8 | P2HP2(H2P4)3H2 |
S1-4 | 36 | -14 | P 3 H 2 P 2 H 2 P 5 H 7 P 2 H 2 P 4 H 2 P 2 HP 2 |
S1-5 | 48 | -23 | P2H(P2H2)2P5H10P6(H2P2)2HP2H5 |
S1-6 | 50 | -21 | H2(PH)3PH4PH(P3H)2P4H(P3H)2PHPH4(HP)3H2 |
S1-7 | 60 | -36 | P 2 H 3 PH 8 P 3 H 10 PHP 3 H 12 P 4 H 6 PH 2 PHP |
S1-8 | 64 | -42 | H12(PH)2(P2H2)2P2HP2H2PPH2P2HP2(H2P2)2(HP)2H12 |
S1-9 | 85 | -53 | H4P4H12P6(H12P3)3HP2(H2P2)2HPH |
S1-10 | 100 | -50 | P3H2P2H4P2H3(PH2)2PH4P8H6P2H6P9HPH2PH11P2H3PH2PHP2HPH3P6H3 |
S1-11 | 100 | -48 | P 6 HPH 2 P 5 H 3 PH 5 PH 2 P 4 H 2 P 2 H 2 PH 5 PH 10 PH 2 PH 7 p 11 H 7 P 2 HPH 3 P 6 HPH 2 |
3D HP | |||
S2-1 | 48 | -32 | HPH 2 P 2 H 4 PH 3 P 2 H 2 P 2 HPH 2 PHPH 2 P 2 H 2 P 3 HP 8 H 2 |
S2-2 | 48 | -34 | H 4 PH 2 PH 5 P 2 HP 2 H 2 P 2 HP 6 HP 2 HP 3 HP 2 H 2 P 2 H 3 PH |
S2-3 | 48 | -34 | PHPH2PH6P2HPHP2HPH2(PH)2P3H(P2H2)2P2H P HP2HP |
S2-4 | 48 | -33 | PHPH2P2HPH3P2H2PH2P3H5P2HPH2(PH)2P4HP2(HP)2 |
S2-5 | 48 | -32 | P2HP3HPH4P2H4PH2PH3P2(HP)2HP2HP6H2PH2PH |
S2-6 | 48 | -32 | H3P3H2PH(PH2)3PHP7HPHP2HP3HP2H6PH |
S2-7 | 48 | -32 | PHP4HPH3PHPH4PH2PH2P3HPHP3H3(P2H2)2P3H |
S2-8 | 48 | -31 | PH2PH3PH4P2H3P6HPH2P2H2PHP3H2(PH)2PH2P3 |
S2-9 | 48 | -34 | (PH)2P4(HP)2HP2HPH6P2H3PHP2HPH2P2HPH3P4H |
S2-10 | 48 | -33 | PH2P6H2P3H3PHP2HPH2(P2H)2P2H2P2H7P2H2 |