QMEAN

HelpCAMEO evaluation

Dopamine Transporter (Created: 3 months ago)Example Archive

Uploaded Structure:shift_in_front_helix_four.pdb ; shift_into_middle.pdb ; original_hhblits_alignment.pdb ; shift_towards_cter.pdb
Method: QMEANBrane
SEQRES:

>A
MNSISDERETWSGKVDFLLSVIGFAVDLANVWRFPYLCYKNGGGAFLVPYGIMLAVGGIPLFYMELALGQHNRKGAITCWGRLVPLFKGIGYAVVLIAFYVDFYYNVIIAWSLRFFFASFTNSLPWTSCNNIWNTPNCRPFESQGFQSAASEYFNRYILELNRSEGIHDLGAIKWDMALCLLIVYLICYFSLWKGISTSGKVVWFTALFPYAALLILLIRGLTLPGSFLGIQYYLTPNFSAIYKAEVWADAATQVFFSLGPGFGVLLAYASYNKYHNNVYKDALLTSFINSATSFIAGFVIFSVLGYMAHTLGVRIEDVATEGPGLVFVVYPAAIATMPASTFWALIFFMMLATLGLDSSFGGSEAIITALSDEFPKIKRNRELFVAGLFSLYFVVGLASCTQGGFYFFHLLDRYAAGYSILVAVFFEAIAVSWIYGTNRFSEDIRDMIGFPPGRYWQVCWRFVAPIFLLFITVYLLIGYEPLTYADYVYPSWANALGWCIAGSSVVMIPAVAIFKLLSTPGSLRQRFTILTTPWRDQQLVPR

Email:user@qmean.ch

Quality for shift_in_front_helix_four.pdb


Model Structure

Sequence colored by local quality:

QMEAN colorbar

Quality for shift_into_middle.pdb


Model Structure

Sequence colored by local quality:

QMEAN colorbar

Quality for original_hhblits_alignment.pdb


Model Structure

Sequence colored by local quality:

QMEAN colorbar

Quality for shift_towards_cter.pdb


Model Structure

Sequence colored by local quality:

QMEAN colorbar
 

Reference for the QMEAN scoring function:
[1] Benkert, P., Tosatto, S.C.E. and Schomburg, D. (2008). "QMEAN: A comprehensive scoring function for model quality assessment." Proteins: Structure, Function, and Bioinformatics, 71(1):261-277.

Reference for the QMEANBrane scoring function:
[2] Studer, G., Biasini, M. and Schwede, T. (2014). "Assessing the local structural quality of transmembrane protein models using statistical potentials(QMEANBrane)." Bioinformatics, 30(17):i505-11.

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.