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Edesign specifications

Information


Unique identifier OMICS_12144
Name Edesign
Interface Web user interface
Restrictions to use None
Input data Sequence (5'->3', string of ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored)
Input format FASTA
License GNU General Public License version 3.0
Computer skills Basic
Version 2.0.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Yasumasa Kimura

Information


Unique identifier OMICS_12144
Name Edesign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.0
Stability Stable
Source code URL https://codeload.github.com/yasumasak/edesign/zip/master
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Yasumasa Kimura

Publication for Edesign

Edesign citations

 (3)
library_books

Highly sensitive detection of a HER2 12 base pair duplicated insertion mutation in lung cancer using the Eprobe PCR method

2017
PLoS One
PMCID: 5289711
PMID: 28152008
DOI: 10.1371/journal.pone.0171225

[…] nd Eprobe for the HER2 12-bp duplicated insertion are shown in . The forward primer was designed to enrich the mutant-type using the principles of allele-specific PCR. A primer and probe design tool (Edesign[]) was used to design all primers and probes.A condition of asymmetric PCR (forward primer: reverse primer = 1:5) was used to detect amplification with Eprobe hybridization. The PCR products w […]

library_books

Risperidone and NAP protect cognition and normalize gene expression in a schizophrenia mouse model

2015
Sci Rep
PMCID: 4639790
PMID: 26553741
DOI: 10.1038/srep16300

[…] to EB1 and EB3. Bioinformatics techniques were applied, developing a model based on EB1–3 and NAP protein structure (). This was followed by screening application on FDA approved drugs directories on Edesign web server. RIS was identified as an EB1/EB3 interacting molecule (). […]

library_books

Design of protein interaction specificity affords selective bZIP binding peptides

2009
Nature
PMCID: 2748673
PMID: 19370028
DOI: 10.1038/nature07885

[…] provably lowest predicted binding energy to a target. Given this sequence, energy gaps between the design•target dimer and al design•competitor dimers, including design•design, are calculated as gap=Edesign:competitor − Edesign:t arg et. The minimal gap (which may be negative) is defined as Δ. In the next iteration of the specificity sweep, the design•target energy is re-optimized, this time impo […]

Citations

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Edesign institution(s)
K.K. DNAFORM, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Kanagawa, Japan; RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Kanagawa, Japan; RIKEN Preventive Medicine & Diagnosis Innovation Program, Wako-shi, Saitama, Japan
Edesign funding source(s)
This work was supported by (1) research grants for RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, (2) a research grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology through RIKEN Preventive Medicine and Diagnosis Innovation Program, and (3) a Research Grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology to the RIKEN Center for Life Science Technologies.

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