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Protocols

Sparky specifications

Information


Unique identifier OMICS_03377
Name Sparky
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format Felix, Bruker or UCSF format.
Output data Text peak lists showing assignments, chemical shifts, volumes, linewidths, etc. Output suitable for structure determination with DYANA or XPLOR, or distance restraint calculation with MARDIGRAS can be generated.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.115
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Thomas Goddard

Sparky citations

 (773)
library_books

Molecular mechanism of influenza A NS1 mediated TRIM25 recognition and inhibition

2018
Nat Commun
PMCID: 5940772
PMID: 29739942
DOI: 10.1038/s41467-018-04214-8

[…] of 800 mhz. samples were measured at concentrations ranging between 0.1 and 0.5 mm in 20 mm na2hpo4, 150 mm nacl, 0.5 mm tcep at ph 6.5. all spectra were processed with nmrpipe and analysed using sparky, ccpnmr and cara (http://cara.nmr.ch). for backbone resonance assignments of the pryspry domain, hncacb, cbca(co)nh and hnca spectra were recorded. backbone resonance assignment was obtained […]

library_books

Structures of chaperone substrate complexes docked onto the export gate in a type III secretion system

2018
Nat Commun
PMCID: 5932034
PMID: 29720631
DOI: 10.1038/s41467-018-04137-4

[…] typically, 0.3 mm isotopically labeled protein samples were prepared in 50 mm napi (ph 6.8), 300 mm nacl, 0.05% nan3, and 10% 2h2o. all recorded spectra were processed with nmrpipe and analyzed with sparky. backbone assignment was accomplished using transverse relaxation optimized spectroscopy (trosy)-based triple resonance experiment. 13cα, 13cβ, 13c′, and backbone 1h and 15n chemical shifts […]

library_books

Conformational dynamics in crystals reveal the molecular bases for D76N beta 2 microglobulin aggregation propensity

2018
Nat Commun
PMCID: 5916882
PMID: 29695721
DOI: 10.1038/s41467-018-04078-y

[…] 15, and 20 khz. examples of decay curves are shown in supplementary fig. ., the nmr data processing was done with topspin, the resonance assignment with cara and the analysis of the relaxation with sparky., all relaxation data fitting has been done using matlab. amide 15n relaxation was assumed to be dominated by the dipolar coupling with its bonded 1h and by its csa. the relaxation rates […]

library_books

The IL 33 PIN1 IRAK M axis is critical for type 2 immunity in IL 33 induced allergic airway inflammation

2018
Nat Commun
PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6

[…] was verified by sds-page., nuclear magnetic resonance (nmr) experiments were performed on a varian inova 600-mhz spectrometer at 25 °c. nmr spectra were processed and analyzed using nmrpipe and sparky software; t. d. goddard and d. g. kneller, sparky 3, university of california, san francisco). the composite chemical shift change in the 2d 1h -15n hsqc was monitored during nmr titration […]

library_books

Modulation of Hoogsteen dynamics on DNA recognition

2018
Nat Commun
PMCID: 5902632
PMID: 29662229
DOI: 10.1038/s41467-018-03516-1

[…] ed with a triple-resonance hcn cryogenic probe; and an 800 mhz varian directdrive2 spectrometer equipped with a triple-resonance hcn cryogenic probe. data were processed and analyzed with nmrpipe and sparky, respectively. resonances were assigned with conventional 2d heteronuclear multiple quantum coherence (hmqc), hsqc, and noesy experiments., 13c and 15n r1ρ rd experiments were performed at 700  […]

library_books

Pursuing origins of (poly)ethylene glycol induced G quadruplex structural modulations

2018
Nucleic Acids Res
PMCID: 5934638
PMID: 29648656
DOI: 10.1093/nar/gky250

[…] 2h2o. twenty different gradient strengths (2.4–59.6 g cm−1) were used in diffusion nmr experiments (dosy). nmr spectra were processed and analysed with the use of vnmrj (varian inc.) software and sparky (ucsf) software ()., noesy spectra with mixing times of 80, 150 and 200 ms were recorded to collect distance restraints for exchangeable and non-exchangeable protons. the noe cross-peaks […]


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