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NMRFAM-SPARKY specifications

Information


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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No version available

Publication for NMRFAM-SPARKY

NMRFAM-SPARKY citations

 (22)
call_split

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
call_split See protocol

[…] using 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 after clea […]

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

[…] g 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. […]

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

[…] sed 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 were obtained […]

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.The backbo […]

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

[…] ure 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 mo […]

call_split

Multivalency regulates activity in an intrinsically disordered transcription factor

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

[…] tware 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). […]

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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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