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Protocols

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 citations

 (248)
library_books

Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

2018
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 […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
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. […]

library_books

HadD, a novel fatty acid synthase type II protein, is essential for alpha and epoxy mycolic acid biosynthesis and mycobacterial fitness

2018
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 […]

library_books

Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

2018
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 […]

library_books

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

2018
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 […]

library_books

Molecular Cloning and Characterization of Carbonic Anhydrase XII from Pufferfish (Takifugu rubripes)

2018
PMCID: 5877703
PMID: 29534037
DOI: 10.3390/ijms19030842

[…] sequence. based on different statistical scores (ga341 and zdope), the best model of ca xii was selected. to further optimize the model, stereoscopic properties were validated with the proq, verify3d, and errat tools. the evaluation results for the ca xii model were as follows. proq, lgscore: 5.873 (value >4 implies an extremely good model) and maxsub: 0.585 (values >0.5–<0.8 […]


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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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