A replica exchange Monte Carlo algorithm for protein folding in the HP model

Thachuk, Chris; Shmygelska, Alena; Hoos, Holger H

doi:10.1186/1471-2105-8-342

BMC Bioinformatics

Table 1 Standard benchmark sequences

From: A replica exchange Monte Carlo algorithm for protein folding in the HP model

ID	Length	E*	Protein Sequence
2D HP
S1-1	20	-9	(HP)₂PH₂PHP₂HPH₂P₂HPH
S1-2	24	-9	H₂(P₂H)₇H
S1-3	25	-8	P₂HP₂(H₂P₄)₃H₂
S1-4	36	-14	P₃H₂P₂H₂P₅H₇P₂H₂P₄H₂P₂HP₂
S1-5	48	-23	P₂H(P₂H₂)₂P₅H₁₀P₆(H₂P₂)₂HP₂H₅
S1-6	50	-21	H₂(PH)₃PH₄PH(P₃H)₂P₄H(P₃H)₂PH₄(PH)₄H
S1-7	60	-36	P₂H₃PH₈P₃H₁₀PHP₃H₁₂P₄H₆PH₂PHP
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	P₆HPH₂P₅H₃PH₅PH₂P₄H₂P₂H₂PH₅PH₁₀PH₂PH₇P₁₁H₇P₂HPH₃P₆HPH₂
3D HP
S2-1	48	-32	HPH₂P₂H₄PH₃P₂H₂P₂HPH₃PHPH₂P₂H₂P₃HP₈H₂
S2-2	48	-34	H₄PH₂PH₅P₂HP₂H₂P₂HP₆HP₂HP₃HP₂H₂P₂H₃PH
S2-3	48	-34	PHPH₂PH₆P₂HPHP₂HPH₂(PH)₂P₃H(P₂H₂)₂P₂HPHP₂HP
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

2D and 3D standard benchmark collection which can be found in [9]. These sequences can be found originally amongst [6, 20]. As presented in [9], H_iand P_iindicate a string of i consecutive H's and P's; likewise (s)_iindicated an i-fold repetition of string s.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com