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RefDB specifications

Information


Unique identifier OMICS_17184
Name RefDB
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/RefDB

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Documentation


Maintainer


  • person_outline Markus Hoenicka

Additional information


Tuto: http://refdb.sourceforge.net/tutorial/refdbtutorial.pdf

RefDB citations

 (17)
library_books

Structural analysis of the complex between influenza B nucleoprotein and human importin α

2017
Sci Rep
PMCID: 5719345
PMID: 29215074
DOI: 10.1038/s41598-017-17458-z

[…]  °c. the spectra were processed with nmrpipe and automatic assignment was done with the program mars and manually verified. secondary chemical shifts were calculated using the random coil values from refdb., a multi-conformational model of b/nptail was calculated based on the chemical shifts as obtained from the assignment using a combination of flexible-meccano and the genetic algorithm asteroids […]

library_books

Gut microbiota composition is associated with environmental landscape in honey bees

2017
Ecol Evol
PMCID: 5756847
PMID: 29321884
DOI: 10.1002/ece3.3597

[…] was used for amplicon sequence processing (hildebrand, tadeo, voigt, bork, & raes, ) using the following optional lotus command line options: “‐p miseq derepmin 8:1,4:2,3:3 –simbasedtaxo 2 –refdb slv thr 8.” the pipeline was used to demultiplex reads with modified quality filtering to accommodate for the increased miseq sequence length, trimming reads to 220 bp, and rejecting reads […]

library_books

Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF κB and transcription regulatory factors

2017
Nucleic Acids Res
PMCID: 5435986
PMID: 28334776
DOI: 10.1093/nar/gkx146

[…] () in p65ta1 free form, bound to tfb1ph and to cbpkix. chemical shifts from 1hn, 1hα, 15nh, 13cα and 13cβ nuclei were used as input data and compared with random-coil chemical shift values from refdb database ()., backbone dihedral angles were obtained using either talosn for tfb1ph () and talos+ (), which gives more accurate predictions for p65ta1. noesy spectra were manually peaked […]

library_books

Structural analysis of a signal peptide inside the ribosome tunnel by DNP MAS NMR

2016
Sci Adv
PMCID: 4991931
PMID: 27551685
DOI: 10.1126/sciadv.1600379

[…] in the spectra of the two variants were compared to averaged chemical shifts for helical, strand-like, or coil-like geometries according to statistics from the protein chemical shift database (refdb; http://refdb.wishartlab.com) (). furthermore, we specifically focused on cross peak patterns of amino acids that do not strongly overlap with others residue types, such as serines […]

library_books

Structural and dynamics studies of a truncated variant of CI repressor from bacteriophage TP901 1

2016
Sci Rep
PMCID: 4941734
PMID: 27403839
DOI: 10.1038/srep29574

[…] under ccpnmr or by mars. an almost complete assignment of the 1hn, 15n, 13cα and 13c’ nuclei was obtained (bmrb id: 26058). secondary chemical shifts were calculated using random coil values from refdb., 15n r1, r2 (cpmg) relaxation experiments were carried out at 298 k on a varian spectrometer operating at a 1h frequency of 600 mhz using a 15n, 13c-labeled sample of ci∆58 (395 μm) and a 15n, […]

library_books

Disentangling the effects of type 2 diabetes and metformin on the human gut microbiota

2015
Nature
PMCID: 4681099
PMID: 26633628
DOI: 10.1038/nature15766

[…] against the silva 119 rrna database and further refined by blast searches against the ncbi rrna database to identify intestinibacter otus, using the following lotus command line options: “-p miseq -refdb slv -doblast blast -amplicon_type ssu -tax_group bacteria -derepmin 2 -cl 2 -thr 14”., microbial taxa where mean abundance over all samples was less than 30 reads, or which were present in less […]


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