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Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations
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10.1063/1.4816641
/content/aip/journal/jcp/139/4/10.1063/1.4816641
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/4/10.1063/1.4816641

Figures

Image of FIG. 1.
FIG. 1.

Comparison between mean-field cavitation forces from explicit solvent and nonpolar terms, (a) SASA, = 0.72 and (b) solute volume, = 0.91.

Image of FIG. 2.
FIG. 2.

Nonpolar solvent force distribution along a single axis for an atom on the surface of a Trp-cage protein decoy.

Image of FIG. 3.
FIG. 3.

Sampling of chignolin structures using different simulation protocols: (a) GBMV + SASA, = 5.42 cal/mol/Å2, = 1.4 Å; (b) GBMV + SASA, = 40 cal/mol/Å2, = 0.7 Å; (c) GBMV + volume, = 30 cal/mol/Å3; (d) TIP3P explicit solvent (−13 400 kcal/mol subtracted from the energies).

Image of FIG. 4.
FIG. 4.

Rescoring with other cavitation term. a) SASA ( = 40 cal/mol/Å2) rescoring of two native basin-visiting windows of the explicit solvent chignolin run. b) Volume term ( = 30 cal/mol/Å3) rescoring of ∼15 000 random structures of the Trp-zip ( = 40 cal/mol/Å2) run ( = 270 K window).

Tables

Generic image for table
Table I.

Nonpolar solvation single parameter fits to unfiltered and filtered mean.

Generic image for table
Table II.

Chignolin folding simulations starting from the conformation: model accuracies (RMSD, Å) and melting temperatures, (K). Experimental is 312 K. 29

Generic image for table
Table III.

Metrics for folding the Trp-cage ( [exp] = 315 K 34 ) and Trp-zip ( [exp] = 323 K 16 ) peptides. SASA parameters: = 40 cal/mol/Å2, = 0.7 Å; Volume parameter: = 30 cal/mol/Å3.

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/content/aip/journal/jcp/139/4/10.1063/1.4816641
2013-07-30
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/4/10.1063/1.4816641
10.1063/1.4816641
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