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A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling
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10.1063/1.2208607
/content/aip/journal/jcp/124/24/10.1063/1.2208607
http://aip.metastore.ingenta.com/content/aip/journal/jcp/124/24/10.1063/1.2208607

Figures

Image of FIG. 1.
FIG. 1.

Illustration of the equi-energy jump.

Image of FIG. 2.
FIG. 2.

Diagram of the EE sampler.

Image of FIG. 3.
FIG. 3.

The pull moves as the mutation move set.

Image of FIG. 4.
FIG. 4.

The normalized mean square error of for various combinations of , the number of distributions employed, and , the number of Monte Carlo steps per distribution. (a) The accuracy for estimating the density of states at the lowest energy of . (b) The accuracy for estimating at the second lowest energy of .

Image of FIG. 5.
FIG. 5.

The Boltzmann averages of (a) BOXSIZE, (b) end-to-end distance, (c) surface-H-number, and (d) surface-P-number at different temperatures of the length-20 protein.

Image of FIG. 6.
FIG. 6.

The Boltzmann averages of (a) BOXSIZE, (b) end-to-end distance, (c) surface-H-number, and (d) surface-P-number at different temperatures of the length-64 protein.

Image of FIG. 7.
FIG. 7.

The Boltzmann average (plus and minus two standard errors) of the surface-P-number of the nine length-50 sequences at different temperatures.

Image of FIG. 8.
FIG. 8.

Two conformations with energy of for seq64 (the length-64 sequence) found by the EE sampler.

Image of FIG. 9.
FIG. 9.

Two conformations with energy of for seq85 (the length-85 sequence) found by the EE sampler.

Image of FIG. 10.
FIG. 10.

Two conformations with energy of for seq100a (the first length-100 sequence) found by the EE sampler.

Image of FIG. 11.
FIG. 11.

Two conformations with energy for seq100b (the second length-100 sequence) found by the EE sampler.

Tables

Generic image for table
Table I.

The normalized density of states estimated from the EE sampler (plus and minus twice the standard error) compared with the actual value for the length-20 protein HPHPPHHPHPPHPHHPPHPH.

Generic image for table
Table II.

The normalized density of states estimated from the EE sampler (plus and minus twice the standard error) for the length-64 protein HHHHHHHHHHHHPHPHPPHHPPHHPPHPPHHPPHHPPHPPHHPPHHPPHPHPHHHHHHHHHHHH.

Generic image for table
Table III.

The nine length-50 sequences together with their hydrophobic residue percentages, minimum energies, and the apparent transition temperatures.

Generic image for table
Table IV.

The nine benchmark sequences. Seq20 to seq85 are taken from Ref. 11. Seq100a and seq100b are taken from Ref. 32.

Generic image for table
Table V.

The performance of the EE sampler in finding the ground states compared with that of GA, EMC, PERM, SISPER, and HuGS. Columns 3–6 are adopted from Ref. 15. Column 7 is adopted from Ref. 12. Column 2 reports the lowest energy achieved by the EE sampler in 15 independent runs. The parameter settings of the EE sampler for the four longest sequences are given in Table VI.

Generic image for table
Table VI.

The parameter settings of the EE sampler for the four longest sequences. Both the temperatures and the energy truncation levels are set by a geometric progressing within the range shown.

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/content/aip/journal/jcp/124/24/10.1063/1.2208607
2006-06-27
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling
http://aip.metastore.ingenta.com/content/aip/journal/jcp/124/24/10.1063/1.2208607
10.1063/1.2208607
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