VERIFY3D protocols

View VERIFY3D computational protocol

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VERIFY3D specifications

Information


Unique identifier OMICS_13694
Name VERIFY3D
Interface Web user interface
Restrictions to use None
Input data A protein structure
Input format PDB
Output data A profile window plot
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline James Bowie <>

Publications for VERIFY3D

VERIFY3D in pipelines

 (4)
2018
PMCID: 5867870
PMID: 29518000
DOI: 10.3390/genes9030149

[…] compared with results of the psipred analysis to ensure their reliability. the assessment of the final structure models was conducted using five independent servers: prosa [,], rampage [], errat [], verify3d [] and qmean []. all the modeled structures were visualized and analyzed using the molecular visualization program pymol (http://www.pymol.org)., to explore whether the proteins involved […]

2015
PMCID: 4337239
PMID: 25755662
DOI: 10.3389/fpls.2015.00091

[…] simulation with simulated annealing, performed by modeler. the quality of the best model was assessed by the determination of its energy (prosaii; ) and local sequence-structure correlation (verify3d; ). in the case of nad+-bound atsdh, the structure of the 18 amino acids at the n-terminus was predicted by jpred3 () and then subjected to ab initio modeling using the galaxyweb server (). […]

2012
PMCID: 3527289
PMID: 22892012
DOI: 10.1186/1471-2091-13-16

[…] the mutations were mapped on the proposed rica structure using macpymol (http://www.pymol.org/). the proposed structure was obtained using esypred3d program [] and verified for correctness using verify3d [] server (http://nihserver.mbi.ucla.edu/verify_3d/)., purified his6-rica was obtained from e. coli bl21 (de3) over-expression clone. a filtered lysate was loaded into a chromatography […]

2008
PMCID: 2475510
PMID: 18670631
DOI: 10.1371/journal.pgen.1000146

[…] by insertions. although h. pylori and d. radiodurans reco share only 14 % identity, a structural model of the h. pylori reco could be generated. the model generated the acceptable prosa2003 and verify3d evaluation methods' scores (-0.59 and 0.31, respectively) with only 7 residues having a negative verify3d score in the (50–55) loop of the protein. evolutionary rates were calculated using […]


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VERIFY3D in publications

 (248)
PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] modelling section was followed by the model analysis section. the stereo chemical quality and structural integrity of the model vp-3 was tested by rampage server () (a), errat (), prosa (; ) and verify3d (; ) softwares and the target–template superimposition is shown in (b) ().fig. 1fig. 1, the modelled structure of vp-3 in complex with an inhibitor leupeptin was worn as beginning structure […]

PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] with the template used to generate the corresponding structure models were selected for subsequent analysis. further the selected protein structure models were checked for their quality using verify3d (http://servicesn.mbi.ucla.edu/verify3d/) and procheck (http://servicesn.mbi.ucla.edu/procheck/) (supplementary table ). thus, good quality structure models of filtered proteins in a. […]

PMCID: 5902629
PMID: 29662082
DOI: 10.1038/s41598-018-24380-5

[…] hada protein (4rlj) (41% sequence identity with msmeg_0948) as a template in the program modeller v9. the model was evaluated through the internal modeller energy score and modeller, qmean, verify3d, dope, dfire and errat softwares. the good scores obtained (e.g. modeller: 604.39; qmean: 0.51) indicated the good quality of the model., the msmeg_0948 gene from m. smegmatis mc²155 […]

PMCID: 5879549
PMID: 29606095
DOI: 10.1186/s12879-018-3068-y

[…] capsid. the selected templates were 1ihm and 4op7. the modeller© v. 9.15 software was used to build the 3d models. after protein modeling, the results were validated using the procheck [] and verify3d programs [] in order to check the biochemical parameter quality. a visual inspection was performed using the pymol molecular graphics system v. 1.8 (schrödinger, llc)., during the period […]

PMCID: 5885017
PMID: 29547094
DOI: 10.1099/mgen.0.000165

[…] meropenem was docked into the models using glide (schrodinger), and the position of the ligands in available crystal structures used to guide placement. the quality of the models was confirmed with verify3d (data not shown). model structures were examined using arpeggio [] and pymol., the structural consequences of the missense variants were analysed to account for all the potential effects […]


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VERIFY3D institution(s)
Laboratory of Structural Biology and Molecular Medicine, University of California, CA, USA
VERIFY3D funding source(s)
This work was supported by National Institutes of Health and Department of Energy.

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