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 in publications

 (17)
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 […]

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 […]

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 […]

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 […]

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, […]


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