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Native protein structures decoy data sets

Two additional decoy data sets of misfolded proteins [17] and of predicted protein structures from the Critical Assessment of Techniques for Protein Stmcture Prediction (CASP) [67] are also used to illustrate the method and its utility. Individual components of the energy perform worse than the total energy for example, for the bulk of the well-packed decoys, the van der Waals energy provides very little information about structural similarity between a well-packed non-native structure and the native state. It is also shown that some aspects of the SGB model results can be mimicked by a screened electrostatic energy, although the SGB approximation provides a better discriminatory measure between non-native and native states. [Pg.462]

Examination of minimized energies for the seven extensive data sets of protein decoys (see Fig. 1) shows that using the OPLS-AA/SGB potential, no decoy scores better than the X-ray structure. The correlation between stractural similarity and score is strong only for structures with low RMSD. For RMSD > 4 A this correlation breaks down. Native-like states appear around 2 A at low energies, with the bulk of the decoys being in non-native-like conformations with RMSD above 4 A. [Pg.466]


See other pages where Native protein structures decoy data sets is mentioned: [Pg.464]    [Pg.464]    [Pg.466]    [Pg.472]    [Pg.481]    [Pg.483]    [Pg.470]    [Pg.473]   
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Data set

Data structure

Decoy

Decoy data set

Decoy structures

Native protein structures

Native structure

Protein structural data

Proteins native

Structural data

Structured data

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