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Elastic network normal modes provide a basis for protein structure refinement
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10.1063/1.4710986
/content/aip/journal/jcp/136/19/10.1063/1.4710986
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/19/10.1063/1.4710986

Figures

Image of FIG. 1.
FIG. 1.

Scheme of construction of the deformation matrix between two structures. Structures are superimposed, and then the i-th element of deformation matrix T is taken as a difference between the coordinates of two corresponding positions. On the picture Q indicates query, and the M modeled structure so that T = QM.

Image of FIG. 2.
FIG. 2.

Distributions and comparisons of various structure quality metrics. Upper triangle: Spearman correlation coefficients between: RMSD, TM-score, LG-score, and Max-Sub score. Diagonal: Density distributions. Lower triangle: Pairwise correlations plots between each measure. Red lines (lower triangle) are averages over all points in bins on abscissa. Red dots correspond to decoys for which TM-score ≥ 0.5, and black dots for these with TM-score ≤ 0.5. Plots are generated for all cluster medoids (see Sec. II).

Image of FIG. 3.
FIG. 3.

An example case for an overlap between thermal motion of decoy structure and deformation from the native state. Picture presents best medoid of 1di2A protein. Native structure is in cartoon representation, colored according its secondary structure elements (purple – helix; yellow – β strand; light green – hairpin; white – loop), and decoy in represented as a blue tube. Combination of the three lowest normal modes in presented as red arrows. In boxes mark two worst modeled structure elements: loop from 14 Gly to 18 Pro and hairpin from 27 Gly to 32 Arg.

Image of FIG. 4.
FIG. 4.

Distributions and comparisons of RMSD, sizes and cumulative overlaps. Upper triangle: Spearman correlation coefficients for: RMSD, Length, COV(20), and COV(5%). Diagonal: The density distributions for each quantity. Lower triangle: Pairwise correlations plots between each measure. Red lines (lower triangle) are averages over all points in bins on abscissa. Red dots correspond to decoys for which TM-score ≥ 0.5, and black dots for cases with TM-score ≤ 0.5. Plots are generated for all cluster medoids (see Sec. II).

Tables

Generic image for table
Table I.

Summary of clustered output. First column is the PDB name of the protein. Italic cases were not considered in later analyses because of poor resolution. The second column is the number of amino acids in the protein. The third column shows the RMSD of the medoid of the first cluster, while the fifth column shows the RMSD for the best medoid among the first top 5 clusters, and the number of that cluster. The fourth and sixth columns show the changes of RMSD after energy minimization. The superscript m denotes a median from the column.

Generic image for table
Table II.

Cumulative overlap table for medoids of the first largest clusters. The first column is the PDB name of the studied protein. The second to fourth columns show cumulative overlaps for the first 3, 6, and 20 slowest modes, respectively. The fifth column show cumulative overlap for 5% of the slowest modes, and the number of those modes. The sixth column shows Spearman correlation coefficient between positional cumulative overlap and B-factor (calculated based on decoy structure) and the seventh column shows Spearman correlation coefficient between positional cumulative overlap and root square deviation (RSD) of every amino acid. The superscript m denotes a median from the column.

Generic image for table
Table III.

Cumulative overlap for the single best medoid from the first five clusters. The first column shows the PDB name of the studied protein. The second column shows the index number of the best cluster (according to COV(20)) and its RMSD. The third to fifth columns show the cumulative overlaps for 3, 6, and 20 slowest modes, respectively. The sixth column shows the cumulative overlap for 5% of the slowest modes, and also the number of these modes. The seventh column shows Spearman correlation coefficient between positional cumulative overlap and B-factor (calculated based on decoy structure) and the eighth column shows Spearman correlation coefficient between positional cumulative overlap and root square deviation (RSD) of every amino acid. The superscript m denotes a median from the column.

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/content/aip/journal/jcp/136/19/10.1063/1.4710986
2012-05-18
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Elastic network normal modes provide a basis for protein structure refinement
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/19/10.1063/1.4710986
10.1063/1.4710986
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