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Amino-acid-dependent main-chain torsion-energy terms for protein systems
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10.1063/1.4774159
/content/aip/journal/jcp/138/6/10.1063/1.4774159
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/6/10.1063/1.4774159

Figures

Image of FIG. 1.
FIG. 1.

α-helicity (a-1) and β-strandness (a-2) of C-peptide and α-helicity (b-1) and β-strandness (b-2) of G-peptide as functions of the residue number at 300 K. These values were obtained from the REMD simulations. Normal and dotted curves stand for the optimized and the original AMBER ff03 force fields, respectively.

Image of FIG. 2.
FIG. 2.

310-helicity (a-1) and π-helicity (a-2) of C-peptide and 310-helicity (b-1) and π-helicity (b-2) of G-peptide as functions of the residue number at 300 K. These values were obtained from the REMD simulations. Normal and dotted curves stand for the optimized and the original AMBER ff03 force fields, respectively.

Image of FIG. 3.
FIG. 3.

α-helicity (a-1) and β-strandness (a-2) of C-peptide and α-helicity (b-1) and β-strandness (b-2) of G-peptide as functions of temperature. These values were obtained from the REMD simulations. Normal and dotted curves stand for the optimized and the original AMBER ff03 force fields, respectively.

Image of FIG. 4.
FIG. 4.

310-helicity (a-1) and π-helicity (a-2) of C-peptide and 310-helicity (b-1) and π-helicity (b-2) of G-peptide as functions of temperature. These values were obtained from the REMD simulations. Normal and dotted curves stand for the optimized and the original AMBER ff03 force fields, respectively.

Image of FIG. 5.
FIG. 5.

Lowest-energy conformations of C-peptide obtained for each replica from the REMD simulations. (a) and (b) are the results of the original AMBER ff03 and the optimized force fields, respectively. The conformations are ordered in the increasing order of energy. The figures were created with DS Visualizer. 47

Image of FIG. 6.
FIG. 6.

Lowest-energy conformations of G-peptide obtained for each replica from the REMD simulations. (a) and (b) are the results of the original AMBER ff03 and the optimized force fields, respectively. The conformations are ordered in the increasing order of energy. The figures were created with DS Visualizer. 47

Tables

Generic image for table
Table I.

Torsion-energy parameters (V n and γ n ) for the main-chain dihedral angles ψ and ζ in Eq. (2) for the original AMBER ff94, ff96, ff99, ff99SB, and ff03 force fields. The values are common among the amino-acid residues for each force field. Only the parameters for non-zero V n are listed.

Generic image for table
Table II.

Hundred proteins used in the optimization of force-field parameters.

Generic image for table
Table III.

Optimized V 1/2 parameters for the main-chain dihedral angles ψ and ζ for the 19 amino-acid residues (except for proline) in Eq. (4) . The rest of the parameters are taken to be the same as in the original ff03 force field (see Table I ). The original amino-acid-independent values are also listed for reference.

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/content/aip/journal/jcp/138/6/10.1063/1.4774159
2013-02-11
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Amino-acid-dependent main-chain torsion-energy terms for protein systems
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/6/10.1063/1.4774159
10.1063/1.4774159
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