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Protocols

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


No version available

Documentation


Publication for EMRinger

EMRinger citations

 (16)
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Structural and immunologic correlates of chemically stabilized HIV 1 envelope glycoproteins

2018
PLoS Pathog
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986
call_split See protocol

[…] density-guided 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 for […]

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Structural basis for energy transduction by respiratory alternative complex III

2018
Nat Commun
PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8
call_split See protocol

[…] m 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. […]

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Cryo EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins

2018
PLoS Pathog
PMCID: 5933801
PMID: 29684066
DOI: 10.1371/journal.ppat.1007009
call_split See protocol

[…] 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 . […]

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3.3 Å resolution cryo EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound

2018
eLife
PMCID: 5819950
PMID: 29460780
DOI: 10.7554/eLife.31502.023
call_split See protocol

[…] ere 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 (). Fi […]

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Cryo EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein

2018
eLife
PMCID: 5962338
PMID: 29726815
DOI: 10.7554/eLife.35946.020
call_split See protocol

[…] s (generated in ProSMART []) was performed in REFMAC5 in order to maintain the secondary structure in regions with poorer map quality. Validation of the model was performed in Coot, Molprobity () and EMRinger (). The goodness of fit of the model to the map was carried out using Phenix (), using a global model-vs-map FSC correlation (). […]

library_books

Electron cryo microscopy structure of the canonical TRPC4 ion channel

2018
eLife
PMCID: 5951680
PMID: 29717981
DOI: 10.7554/eLife.36615.029

[…] 3, 320 and 323, 389, 390, 649 and 651, 661 and 695, 728 and 730. Finally, we used Molprobity () to validate the overall geometry of the model, Phenix () to calculate the model-to-map correlation, and EMRinger () to validate the side chain geometry. The densities corresponding to annular lipids were modelled as phosphatidic acid lipid with a shorter lipid tail (PDB-ID 44E) and CHS (PDB-ID YO1). The […]

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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

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