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DED specifications


Unique identifier OMICS_20971
Name DED
Alternative name Database of Evolutionary Distances
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained No


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio


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Publication for Database of Evolutionary Distances

DED citations


Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification

PLoS One
PMCID: 5919621
PMID: 29698455
DOI: 10.1371/journal.pone.0196632
call_split See protocol

[…] ec with Whatman # 1 filter paper at 100% humidity at 22°C. Imaging was conducted on a Tecnai F30 Polara (FEI, Hillsboro, OR) microscope operating at 300 kV, with a Gatan K2 Summit electron detection (DED) camera (Gatan, Pleasanton, CA) in super resolution mode. Images were then binned down 2x to achieve a pixel size of 2.635 Å, using SerialEM version 3.6 []. Tilt series were collected using a bidi […]


Predictors of Dietary Energy Density among Preschool Aged Children

PMCID: 5852754
PMID: 29415480
DOI: 10.3390/nu10020178

[…] k, NY, USA), descriptive analysis was conducted to assess participants’ characteristics. Bivariate linear regression models were performed to examine the association between individual predictors and DED with adjustment for covariates including child sex, child age and treatment arm. Multivariable regression models including the previously described potential confounders were conducted to assess i […]


Cryo EM structure of Saccharomyces cerevisiae target of rapamycin complex 2

Nat Commun
PMCID: 5700991
PMID: 29170376
DOI: 10.1038/s41467-017-01862-0
call_split See protocol

[…] 40 frames (0.5 s per frame) with a accumulated total dose of 47 e/Å2 were recorded semi-automatically using SerialEM at a nominal magnification of ×105,000 in super-resolution mode. Images were recorded with a defocus range of −1.5 μm to −3.5 μm. Subsequently, cropping in Fourier space resulted in a pixel size of 1.35 Å.The movie frames from the Falcon II DED were aligned, dose-filtered and summe […]


The Semaphorin 3A inhibitor SM 345431 preserves corneal nerve and epithelial integrity in a murine dry eye model

Sci Rep
PMCID: 5686158
PMID: 29138447
DOI: 10.1038/s41598-017-15682-1

[…] luate the expression of TRPV1, we calculate the percentage of TRPV1 positive areas in the corneal epithelium using the ImageJ software (Fig. ). The expression of TRPV1 was significantly larger in the DED-SM-345431 group (16.5 ± 1.7%) compared to the DED-vehicle group (7.7 ± 2.4%) (p = 0.04, one way ANOVA and Bonferroni post hoc) (Fig. ).Figure 5 […]


Achieving better than 3 Å resolution by single particle cryo EM at 200 keV

Nat Methods
PMCID: 5679434
PMID: 28991891
DOI: 10.1038/nmeth.4461
call_split See protocol

[…] s saved in Leginon and remained unchanged throughout data collection. The objective aperture was centered and any objective lens astigmatism was minimized. Exposure rate measurements on the K2 Summit DED were then collected to determine whether changes to spot size were necessary to achieve the desired exposure rate. In the event that changes in exposure rate were required, as was the case for inc […]


Caspase 8, association with Alzheimer’s Disease and functional analysis of rare variants

PLoS One
PMCID: 5630132
PMID: 28985224
DOI: 10.1371/journal.pone.0185777

[…] The 479 aa protein procaspase-8 isoform 1, including its domains, active sites and mutations that were studied for function, is graphically presented in . Model structures of caspase-8 including DED2 and p18 domains were generated using Phyre2, a web-based tool for predicting and analyzing protein structure and function []. These domain models revealed that caspase-8 residues Lys148 and Ile29 […]


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DED institution(s)
Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA, USA

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