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NMRFAM-SPARKY specifications

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Unique identifier OMICS_06813
Name NMRFAM-SPARKY
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for NMRFAM-SPARKY

NMRFAM-SPARKY citations

 (20)
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

[…] the 1h-15n noesy, 1h-13c aliphatic noesy, and 1h-13c aromatic noesy spectra. carbonyl resonances were assigned using the hnco spectrum., resonance assignments were obtained using pine imbedded in nmrfam-sparky and were adjusted manually. the assigned residue numbers are five added to the original irak-m residue numbering due to the non-native 5 residues at the n-terminus that remain […]

library_books

Rescue of conformational dynamics in enzyme catalysis by directed evolution

2018
Nat Commun
PMCID: 5883053
PMID: 29615624
DOI: 10.1038/s41467-018-03562-9

[…] the 4% methanol + 96% methanol-d4 sample (dlm-5007, cambridge isotope laboratories). all data sets were processed with the nmrpipe/nmrdraw software package and visualized/analyzed using the program nmrfam-sparky., trosy-versions of a 3d hncacb and cbca(co)nh experiments were recorded at 25 °c to obtain a nearly complete sequential backbone resonance assignment (hn, n, cα, cβ) of cypa s99t/c115 […]

library_books

Theoretical and NMR Conformational Studies of β Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units

2018
PMCID: 5883087
PMID: 29644215
DOI: 10.3389/fchem.2018.00091

[…] by nmrpipe (delaglio et al., ) using standard protocol that includes the lorentz-to-gauss window function, forward-backward linear prediction and polynomial baseline correction, and analyzed with nmrfam-sparky (lee et al., ). experimental details of nmr measurements and 1h and 13c signal assignments were reported earlier (kudryavtsev et al., ). most of the noe distance restraints […]

library_books

ISCU(M108I) and ISCU(D39V) Differ from Wild Type ISCU in Their Failure To Form Cysteine Desulfurase Complexes Containing Both Frataxin and Ferredoxin

2018
Biochemistry
PMCID: 5842376
PMID: 29406711
DOI: 10.1021/acs.biochem.7b01234

[…] contained 20 mm hepes (ph 7.6), 150 mm nacl, 2 mm tcep, and 7% d2o as an nmr lock signal. all sample temperatures were regulated at 25 °c. nmrpipe software was used to process the raw nmr data, and nmrfam-sparky software was used to visualize and analyze the processed nmr data. all nmr experiments were performed once except for the nmr titration experiments, which were performed twice., […]

library_books

The Structure of Metal Binding Domain 1 of the Copper Transporter ATP7B Reveals Mechanism of a Singular Wilson Disease Mutation

2018
Sci Rep
PMCID: 5766562
PMID: 29330485
DOI: 10.1038/s41598-017-18951-1

[…] calculation was done using ponderosa-c/s with xplor-nih based calculation options. noe cross peaks were automatically assigned with audana and manually verified by ponderosa analyzer coupled with nmrfam-sparky and pymol (schroedinger llc). final structure calculation step was carried out with explicit water refinement option with validated restraints that selects best 20 from 100 calculated […]

library_books

Multivalency regulates activity in an intrinsically disordered transcription factor

2018
eLife
PMCID: 5963919
PMID: 29714690
DOI: 10.7554/eLife.36258.028

[…] for data processing is available online at the warsaw university laboratory (nmr.cent3.uw.edu.pl/software)). all spectra were analyzed with the graphical nmr assignment and integration software nmrfam-sparky (rrid:scr_014228)., hlbd at a concentration of 30 μm was incubated with 600 μm lc8 at various molar ratios: (hlbd:lc8) 1:3, 1:5, 1:7, 1:9, 1:11, and 1:13. the complex was loaded […]


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NMRFAM-SPARKY institution(s)
National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA

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