HelpCAMEO evaluation

Ornithine Carbamoyltransferase (Created: 5 months, 1 week ago)Example Archive

Uploaded Structure:model_01.pdb ; model_02.pdb ; model_03.pdb
Method: QMEAN



Quality for model_01.pdb

Model Structure
QMEAN4 Value: 0.37

Sequence colored by local quality:

QMEAN colorbar

Quality for model_02.pdb

Model Structure
QMEAN4 Value: -1.07

Sequence colored by local quality:

QMEAN colorbar

Quality for model_03.pdb

Model Structure
QMEAN4 Value: -1.53

Sequence colored by local quality:

QMEAN colorbar

Reference for the QMEAN scoring function:
[1] Benkert, P., Biasini, M., Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343-350 (2011).

Reference for the QMEANDisCo scoring function:
[2] Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).

Reference for the QMEANBrane scoring function:
[3] Studer, G., Biasini, M., Schwede, T. Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics 30, i505-11 (2014).

A single model method combining statistical potentials and agreement terms in a linear manner
Adding distance constraint score to QMEAN to improve local quality predictions. Evaluated are consistencies of pairwise CA-CA distances from a model with constraints extracted from homologous structures
QMEANBrane is a combination of statistical potentials targeted at local quality estimation of membrane protein models in their naturally occurring oligomeric state: after identifying the transmembrane region using an implicit solvation model, specifically trained statistical potentials get applied on the different regions of a protein model
Reference sequence (SEQRES) of submitted protein model. This sequence is used for secondary structure and solvent accessibility predictions. If not provided, the sequence gets directly extracted from the model. See the help page for further input information.
The plot relates the obtained global QMEAN4 value to scores calculated from a set of high-resolution X-ray structures.
Local quality is either estimated using the raw QMEAN scoring function or one of the two specialized functions QMEANBrane and QMEANDisCo. They all provide scores in range [0,1] with one being good.
The value of the QMEAN4 is not affected by DisCo.