ProQ protocols

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ProQ specifications


Unique identifier OMICS_11945
Name ProQ
Interface Web user interface
Restrictions to use None
Input data A protein model and an amino acid sequence.
Input format PDB,FASTA
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Arne Elofsson <>
  • person_outline Bjorn Wallner <>

Publications for ProQ

ProQ in pipelines

PMCID: 4912509
PMID: 27386259
DOI: 10.1186/s40064-016-2443-7

[…] full fhglm was constructed applying ab initio poing 1.0 approach due to lack of templates appropriate for the complete sequence (jefferys et al. ). to check the overall and local quality of models, proq2 assessment was applied within the phyre 2 investigator option thereby the best-scored model was selected. pymol was used to view the homology models ( for recognition […]

PMCID: 5056895
PMID: 27729840
DOI: 10.5808/GI.2016.14.3.104

[…] prosa program (protein structure analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures [], and proq is a neural network based predictor that based on a number of structural features predicts the quality of a protein model []. further the refined model was verified by errat server, errat […]

PMCID: 5056903
PMID: 27729839
DOI: 10.5808/GI.2016.14.3.96

[…] for sialic acid cleavage from glycans of the infected cell. we employed amino acid sequence of h1n1 na to predict the tertiary structure using phyre2 server and validated using procheck, prosa, proq, and errat server. further, the modelled structure was docked with thirteen natural compounds of plant origin using autodock4.2. most of the natural compounds showed effective inhibitory […]

PMCID: 4632066
PMID: 26384370
DOI: 10.1534/g3.115.020180

[…] was built up by using phyre2 based on the best reference. the refinement of the structure was done with modrefiner (). the quality of the predicted model was evaluated by two widely used programs proq () and anolea (). mapping of consensus sequence to the surface of the structure was performed using chimera (). the superposition of the structure of mtrh and metr was performed using superpose […]

PMCID: 4013662
PMID: 24758925
DOI: 10.3390/ijms15046797

[…] atpase domain of human heat shock 70 kda protein 1 (pdb: 1 hjo) were mutated. 3d mutant models (k71l and t204v) using pymol software were then constructed. the structures were evaluated by procheck, proq, errat, verify 3d and prosa modules. all evidence suggests that all protein models are acceptable and of good quality. the e1a32 kda motif was retrieved from uniprot (p03255), as well […]

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ProQ in publications

PMCID: 5928492
PMID: 29732450
DOI: 10.1021/acsomega.7b02007

[…] at 310 k and 1 bar. configurations were taken from these trajectories at 500 ps intervals (0.5 ns) and assessed using three separate methods for quantifying the model quality: rampage, errat, and proq. for this purpose, we calculate the average score for the corresponding trajectory. if this score is below the cutoff value for any of the three methods, the initial structure is refined using […]

PMCID: 5819190
PMID: 29463214
DOI: 10.1186/s12864-018-4549-5

[…] of various factors such as overall g-factor, number of residues in core allowed, generously allowed and disallowed regions in ramachandran plot. we further analyzed the model by qmean [], lgscore in proq [] and z-score in prosa []., the sequences were submitted to a bidimensional eletrophoresis in silico using the jvirgel 2.0 [] to predict the theoretical pi (isoelectric point) and mw (molecular […]

PMCID: 5817056
PMID: 29491860
DOI: 10.3389/fmicb.2018.00233

[…] template was decided for specific protein modeling based on the score interpreted by hhpred. moreover, the quality of the constructed tertiary structure of the protein model was assessed by the proq server ( (wallner and elofsson, )., both mycth_56237 (672 bp) and mycth_49824 (693 bp) display sequence identity with endo-β-1,4-xylanases belonging to gh11 […]

PMCID: 5615308
PMID: 28952541
DOI: 10.3390/bioengineering4030062

[…] 0 and 1). furthermore, a ramachandran plot analysis using the phyre 3d predicted model indicated that 92.3% of the residues are found to be in favored region, with only 2.4% in outlier region (c). proq2 results were similar to gmqe, placing the predicted nag_mgrv-met 3d between moderate to good quality (d)., catalytic sites were confirmed on the phyre predicted model (e,f). the consensus motif […]

PMCID: 5397484
PMID: 28473815
DOI: 10.3389/fmicb.2017.00674

[…] using different templates, obtained from pdb database, based on their homology with the target sequences. the models generated were analyzed for quality check using prosa (wiederstein and sippl, ), proq (wallner and elofsson, ) and rampage (abagyan et al., ) online servers. molecular docking of the best models was done with laccase substrates, i.e., abts, o-tolidine and guaiacol using molsoft […]

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ProQ institution(s)
Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden; Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Solna, Sweden; Department of Physics, Chemistry and Biology (IFM)/Bioinformatics, Linköping University, Linköping, Sweden
ProQ funding source(s)
Supported by grants from the Swedish Research Council (VR-NT 2012-5046 and 2012-5270) and Swedish e-Science Research Center (SeRC).

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