Chemistry Reference
In-Depth Information
Table 7.1
Benchmark HP sequences used in this text
Seq. code
Reference
Sequence
2D50
[
15
]
HHPHPHPHPHHHHPHPPPHPPPHPPPPHPPPHPPPHPH
HHHPHPHPHPHH
2D60
[
15
]
PPHHHPHHHHHHHHPPPHHHHHHHHHHPHPPPHHHHH
HHHHHHHPPPPHHHHHHPHHPHP
2D64
[
15
]
HHHHHHHHHHHHPHPHPPHHPPHHPPHPPHHPPHHPP
HPPHHPPHHPPHPHPHHHHHHHHHHHH
2D85
[
16
]
HHHHPPPPHHHHHHHHHHHHPPPPPPHHHHHHHHHHH
HPPPHHHHHHHHHHHHPPPHHHHHHHHHHHHPPPHPP
HHPPHHPPHPH
2D100a
[
17
]
PPPPPPHPHHPPPPPHHHPHHHHHPHHPPPPHHPPHH
PHHHHHPHHHHHHHHHHPHHPHHHHHHHPPPPPPPPP
PPHHHHHHHPPHPHHHPPPPPPHPHH
2D100b
[
17
]
PPPHHPPHHHHPPHHHPHHPHHPHHHHPPPPPPPPHH
HHHHPPHHHHHHPPPPPPPPPHPHHPHHHHHHHHHHH
PPHHHPHHPHPPHPHHHPPPPPPHHH
3D42
[
18
]
PHHPHPHHPHPHPPHHHPHPHHPHPHHHPPHPHPHHP
HPHHP
3D48
[
19
]
PHPHPPPPHPHPHPPHPHHHHHHPPHHHPHPPHPHHP
PHPHHHPPPPH
3D67
[
18
]
PHPHHPHHPHPPHHHPPPHPHHPHHPHPPHHHPPPHP
HHPHHPHPPHHHPPPHPHHPHHPHPPHHHP
3D88
[
20
]
PHPHHPHHPHPPHHPPHPPHPPHPPHPPHPPHHPPHHH
PPHHHPPHHHPPHHHPPHPHHPHHPHPPHPPHPPHHP
3D103
[
21
]
PPHHPPPPPHHPPHHPHPPHPPPPPPPHPPPHHPHHP
PPPPPHPPHPHPPHPPPPPHHHPPPPHHPHHPPPPPH
HPPPPHHHHPHPPPPPPPPHHHHHPPHPP
3D124
[
21
]
PPPHHHPHPPPPHPPPPPHHPPPPHHPPHHPPPPHPP
PPHPPHPPHHPPPHHPHPHHHPPPPHHHPPPPPPHHP
PHPPHPHPPHPPPPPPPHPPHHHPPPPHPPPHHHHHP
PPPHHPHPHPHPH
3D136
[
21
]
HPPPPPHPPPPHPHHPHHPPPPHPHHHPPPPHPHPHH
HHPPPPPPPPPPPHPPHPPPHPHHPPPHHPPHPPHPH
PHPPPPPPPPHPPPHHHHHHPPPHHPPHHHPPPHHPH
HHHHPPPPPPPPPHPPPPHPHPPPP
7.2.2 Numerical Methods
Previous work showed that the knowledge of the free energy landscape and the ther-
modynamics of a protein system is essential to completely understand the folding
process [
2
,
22
,
23
], and thus Monte Carlo (MC) methods are indispensable tools
for this purpose [
24
]. The configurations of a polymer may be studied using the
traditional Metropolis method [
25
], but the complexity of the resultant free energy
surface at low temperature renders the method extremely inefficient [
26
]. Two
approaches have been taken to resolve the problem. One is to search only for the
ground state configuration with the lowest energy, e.g., MC with minimization
[
27
], simulated annealing [
28
], genetic algorithms [
15
], pruned-enriched Rosen-
bluth method (PERM) [
29
] and its variants [
30
,
31
], tabu search [
32
], evolution-
