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Citations per year

Number of citations per year for the bioinformatics software tool EM-Bfactor
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This map represents all the scientific publications referring to EM-Bfactor per scientific context
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Protocols

EM-Bfactor specifications

Information


Unique identifier OMICS_26526
Name EM-Bfactor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some 3D maps, FSC curves.
Input format MRC,Spider,PIF,EM,Xmipp,Frealign,Bsoft
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Jose-Jesus Fernandez
  • person_outline Jose Fernandez

Publication for EM-Bfactor

EM-Bfactor citations

 (7)
call_split

Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo EM at 6 Å resolution

2016
Sci Adv
PMCID: 5045269
PMID: 27704041
DOI: 10.1126/sciadv.1600058
call_split See protocol

[…] e final reconstruction. For the final reconstruction, we used the “gold standard” procedure (), which involves computing two independent reconstructions in parallel. The final map was sharpened using EM-BFACTOR (), which reweights the reconstruction transform based on the Fourier shell correlation curve and then low-pass–filters it to a corresponding resolution to show each part’s structure.Althou […]

library_books

A combined cryo EM and molecular dynamics approach reveals the mechanism of ErmBL mediated translation arrest

2016
Nat Commun
PMCID: 4935803
PMID: 27380950
DOI: 10.1038/ncomms12026

[…] age resolution of 3.6 Å (0.143 FSC) and a local resolution extending towards 3.0 Å for the core of the 30S and 50S subunits as computed using ResMap (). The final maps were subjected to the programme EM-BFACTOR in order to apply an automatically determined negative B-factor for sharpening of the map. […]

library_books

Structure of a human translation termination complex

2015
Nucleic Acids Res
PMCID: 4605324
PMID: 26384426
DOI: 10.1093/nar/gkv909

[…] requency-limited (truncation of frequencies higher than 8 Å) refinement protocol was used to prevent potential over-fitting (). The final volume was subjected to B-factor sharpening using the program EM-BFACTOR (). […]

library_books

Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid

2015
J Virol
PMCID: 4621102
PMID: 26311868
DOI: 10.1128/JVI.01353-15

[…] hell correlation (FSC) of 0.143 and a resolution of 8.97 Å at an FSC of 0.5 (see Fig. S1 in the supplemental material). The final map was sharpened by applying a B factor of −610.88, as calculated by EM-BFACTOR (). Densities corresponding to individual gp23 subunits were segmented with the Segger extension of UCSF Chimera (, ). Local resolution estimation was prepared with the two half-maps from t […]

library_books

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species specific stalling

2015
Nat Commun
PMCID: 4423224
PMID: 25903689
DOI: 10.1038/ncomms7941

[…] aining the signal recognition particle bound to the ribosome (158,726 particles; 30%), which will be described elsewhere (Beckert et al., unpublished). The final volumes were subjected to the program EM-BFACTOR in order to apply an automatically determined negative B-factor for sharpening of the map. […]

call_split

Acetylcholine Binding Protein in the Hemolymph of the Planorbid Snail Biomphalaria glabrata Is a Pentagonal Dodecahedron (60 Subunits)

2012
PLoS One
PMCID: 3423370
PMID: 22916297
DOI: 10.1371/journal.pone.0043685
call_split See protocol

[…] t least partially represent noise bias. The final density map (5.8 Å resolution) was calculated from 8347 selected particles. A negative temperature factor of 375.84 Å2 was applied using the software EM-BFACTOR , . The resulting 3D reconstruction (see ) was low-pass filtered to 6 Å. […]


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EM-Bfactor institution(s)
Centro Nacional de Biotecnologia, CSIC. Campus Universidad Autonoma, Cantoblanco, Madrid, Spain; Department of Computer Architecture, University of Almeria, Almeria, Spain
EM-Bfactor funding source(s)
Supported by EU-FP6-LSHG-CT-2004-502828, MEC-TIN2005-00447, MEC-BFU2005-06487 and JA-P06-TIC1426.

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