EMRinger statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left 3D macromolecule reconstruction Single particle analysis chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

EMRinger specifications

Information


Unique identifier OMICS_09774
Name EMRinger
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Publication for EMRinger

EMRinger in pipeline

2018
PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8

[…] this work and t. thermophilus caa3 oxygen reductase—pdb 2yev). model building was performed with coot and real space refinement was performed in phenix followed by manual rebuilding. molprobity and emringer were used for model validation. local resolution was estimated using resmap. figures were drawn with ucsf chimera., identification of proteins present in the aciii sample was performed using […]


To access a full list of citations, you will need to upgrade to our premium service.

EMRinger in publications

 (19)
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] rebuild-and-refinement in the rosetta software suite []. rosetta models were manually adjusted in coot followed by evaluation based on geometry (molprobity []) and cryo-em density fit (emringer []). upon convergence, the best model underwent iterative all-atom rosetta refinement and manual rebuilding constrained by the cryo-em density map and with distance constraints introduced […]

PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8

[…] this work and t. thermophilus caa3 oxygen reductase—pdb 2yev). model building was performed with coot and real space refinement was performed in phenix followed by manual rebuilding. molprobity and emringer were used for model validation. local resolution was estimated using resmap. figures were drawn with ucsf chimera., identification of proteins present in the aciii sample was performed using […]

PMCID: 5933801
PMID: 29684066
DOI: 10.1371/journal.ppat.1007009

[…] were carried out iteratively until there were no further improvements in geometry parameters and model-map correlation coefficient. the quality of the final model was analyzed with molprobity [] and emringer []. the validation statistics of the structural models are summarized in ., ibv pseudovirus entry assay was carried out as previously described []. briefly, full-length ibv spike gene […]

PMCID: 5847487
PMID: 29092773
DOI: 10.1016/j.jsb.2017.10.010

[…] same map with phenix.real_space_refine (, ) using icosahedral constraints, secondary structure restraints and reciprocal space b-factor refinement. the refined model was validated by molprobity (), emringer () and cablam () through phenix (). molprobity () compares local geometric features describing an all-atom model to those from high-resolution crystal structures. emringer () validates […]

PMCID: 5819950
PMID: 29460780
DOI: 10.7554/eLife.31502.023

[…] modeled with an octahedrally coordinated mg2+ ion to three water molecules, restrained to ideal distances (2.1 å) and angles (90°). model quality was evaluated using molprobity (), cablam (), and emringer () (). the final model is a good fit to the map () and contains two residues of tag, residues 1 through 743 of the 792 residues of human α, twelve datp molecules, and six cdp molecules (). […]


To access a full list of publications, you will need to upgrade to our premium service.

EMRinger institution(s)
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Graduate Group in Biophysics, University of California, San Francisco, San Francisco, CA, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA; Department of Biochemistry, University of Washington, Seattle, WA, USA; Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Institute for Protein Design, Seattle, WA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA

EMRinger reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review EMRinger