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Workunit: P000002 QMEAN Example

Model of the ADP-ribosylation factor-like protein 6 generated by the ROBETTA server during the CASP7 experiment (target T0308). The model has a C-alpha RMSD of 4 A and a GDT_TS score of 75. The predicted local errors by QMEAN agree quite well with the real deviation from the experimental structure which has been released after the experiment (PDB identifier 2H57).

[QMEAN]

Local Scores:

If you publish results from QMEAN, please cite the following paper:
Benkert, P., Schwede, T. and Tosatto, S.C.E. (2009). QMEANclust: Estimation of protein model quality by # combining a composite scoring function with structural density information. BMC Struct Biol. 2009 May 20;9:35.

QMEAN6:

Global scores Local scores

QMEANscore6
Global score of the whole model reflecting the predicted model reliability ranging from 0 to 1.
Estimated absolute model quality
The QMEAN Z-score is a measure for the absolute quality of a model. The QMEAN score of the model is compared to scores of high-resolution reference structures solved by X-ray crystallography and a Z-score is calculated (see help for more details).
Score components
Z-score of the individual components of QMEAN. The average Z-score of high-resolution structures is 0.
Coloring by residue error
Estimated per-residue inaccuracy visualised using a colour gradient from blue (more reliable regions) to red (potentially unreliable regions).
Residue error plot
Local Model reliability with estimated per-residue inaccuracies along the sequence.

0.687
Z-Score: -0.741
Plot 1: [save png]
Plot 2: [save png]

[save png]

[save png]

All residues error:
[save jpg] [save pdb] Energy profile:
The local model quality data are also provided as tables in tab-separated format. The table contains for each residue the local QMEAN score as well as the values of the terms contributing to it.

[save raw scores]

The QMEAN6 score is a composite score consisting of a linear combination of 6 terms (estimated model reliability between 0-1). The pseudo-energies of the contributing terms are given below together with their Z-scores with respect to scores obtained for high-resolution experimental structures of similar size solved by X-ray crystallography:
Scoring function term Raw score Z-score
C_beta interaction energy -139.36 1.02
All-atom pairwise energy -6893.94 0.74
Solvation energy -12.43 -0.51
Torsion angle energy -30.95 -1.16
Secondary structure agreement 84.2% 0.21
Solvent accessibility agreement 75.2% -0.55
QMEAN6 score 0.687 -0.74

References:

If you publish results from QMEAN, please cite the following paper:
Benkert P, Biasini M, Schwede T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics, 27(3):343-50.

If you publish results using SWISS-MODEL, please cite the following papers:
Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201.

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