Protein Volume Evaluation PROVE

PROVE compares the atomic volumes of a protein model with standard atomic volume values derived from the set of 64 protein structures. Using the same Voronoi methods, the atomic volumes of the protein model under consideration are computed and compared with the normal atomic volumes. The difference between the standardized volumes and the protein model being studied is reported as two different types of Z-scores. The first Z-score involves a comparison between individual atom types as defined in Eq. [7]  

In this equation, the volume of the individual atom (i)is Vf and k indicates the atom type. The mean volume of that atom type is V, and is the standard deviation of that atom type. When an atom has a larger than average volume, it has a positive Z-score. The opposite is true for a smaller than average atom that would have a negative Z-score the ideal Z-score is zero. The second Z-score, called the Zrmsdj involves the comparison of volumes for all atoms or for groups of atoms (in residues). The Zrmsd is calculated as in Eq. 

Deviations of atomic volumes do not indicate directly that a defective protein exists because deviations in atomic volumes can be attributed to other physical phenomena. It is for this reason that the authors of PROVE correlated the atom volume deviations with crystallographic qualities of the protein X-ray structure including the resolution (lowest resolvable separation between two carbon atoms), the R-factor (measure of how well the refined structure agrees with the experimental model/electron density maps/raw data), and B-factors (isotropic temperature factor).A test set of 900 protein structures was constructed, each containing a minimum of 100 buried atoms. The resolution of the protein structures ranged from 1.0 to 3.9 A. The authors found that for high-resolution structures (1.0 to 1.6 A), the average Zrmsd was approximately 1.0. When poorer quality crystal structures were considered, the Zrmsd increased. The correlation coefficient for a plot of Zrmsd versus experimental resolution was 0.89 for all protein structures in the test set 

Using PROVE as a protein model evaluator is beneficial because it provides an alternative method of assessing the validity of proposed structures. As demonstrated by the developers of PROVE, it can predict which structures (and regions of structures) are defective based on resolution, B-factors, and to a lesser extent R-factors, all experimentally derived values that gauge the quality of a structure determined through X-ray crystallography. 

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PROSA II PROVE Verify3D Program to evaluate the fold of protein structures Program for protein volume evaluation Program to evaluate the amino acid side-chain environment (solvent accessibility) of protein... 

In which the ratio m/n is close to 3. The silane was produced by free radical copolymerization of vinyltriethoxysilane with N-vinylpyrrolidone. Its number-average molecular weight evaluated by vapour-phase osmometry was 3500. Porous silica microballs with a mean pore diameter of 225 A, a specific surface area (Ssp) of 130 m2/g and a pore volume of 0.8 cm3/g were modified by the silane dissolved in dry toluene. After washings and drying, 0.55% by weight of nitrogen and 4.65% of carbon remained on the microballs. Chromatographic tests carried out with a series of proteins have proved the size-exclusion mechanism of their separation. 

Hinds and Levitt developed an even coarser-grained model, which proved to emulate small proteins reasonably well, despite its simplicity. Multiple occupancies of lattice sites were permitted in the sense that zero to three residues were placed between the adjacent sites of a tetrahedral lattice. Exhaustive enumeration of all conformations for proteins occupying up to 40 vertices were possible by this approach. Optimal alignment of residues between vertices, elimination of extended conformations by a volume constraint, and evaluation of the resulting conformations on the basis of knowledge-based contact energies, led to folds that could capture the overall path of the native structures. 

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