VERIFY3D pipeline

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)
2017
PMCID: 5535262
PMID: 28824557
DOI: 10.3389/fmicb.2017.01409

[…] of these csis, the 2 aa insert also appears to extend a helix. the current model is in agreement with secondary structure analyses (psipred/concord), and yielded reassuring measurements by errat, verify3d, rampage and prosa. the locations of these csis in the structure of the b. longum nrde subunit indicate that they are topologically distant from the dimer interface/allosteric regulatory […]

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

[…] with simulated annealing, performed by modeler. the quality of the best model was assessed by the determination of its energy (prosaii; sippl, 1993) and local sequence-structure correlation (verify3d; eisenberg et al., 1997). in the case of nad+-bound atsdh, the structure of the 18 amino acids at the n-terminus was predicted by jpred3 (cole et al., 2008) and then subjected to ab initio […]

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 [13] and verified for correctness using verify3d [14] 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 […]

2012
PMCID: 3573378
PMID: 23492818
DOI: 10.4103/0975-1483.104370

[…] protein data bank [figure 1]., the φ and ψ distribution value of the ramachandran plot of non-glycine and non-proline residues are shown in figure 2 and table 1., the profile score above zero in the verify3d graph correspond to the acceptable environment of the model [figure 3]. the global quality of the model for the target sequence was estimated by the qmean6 score based on linear combination […]

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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