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chevron_left Secondary structure prediction Resonance assignment chevron_right
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PINE-SPARKY specifications

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Unique identifier OMICS_03378
Name PINE-SPARKY
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PINE-SPARKY

PINE-SPARKY in publications

 (7)
PMCID: 5925765
PMID: 29281006
DOI: 10.1093/bioinformatics/btx785

[…] conformational changes, internal dynamics and protein–ligand interactions. as a means for facilitating the handling and analysis of spectra involved in these types of nmr studies, we have developed pine-sparky.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. the graphical user interface of pine-sparky.2 […]

PMCID: 5679652
PMID: 29084221
DOI: 10.1371/journal.pgen.1007084

[…] for rdc measurements., signals for sequence-specific backbone resonance assignments were detected by apes [] and assigned by pine algorithm [], and followed with subsequent manual verification by pine-sparky []. due to tev cleavage site introduced into purification constructs, gefgs is present at the n-terminus, followed by the methionine at position 1 of the native ydj1 protein sequence. […]

PMCID: 5454022
PMID: 28572671
DOI: 10.1038/s41598-017-02690-4

[…] go. all collected spectra were processed and analyzed via xwin nmr (bruker instruments, karlsruhe, germany), nmrpipe/nmrdraw (biosym/molecular simulation, inc. san diego, ca, usa) software, and the pine-sparky program., circular dichroism (cd) spectroscopic studies– were performed using a j-815 spectrophotometer (jasco, japan) equipped with a peltier system for controlling the temperature. […]

PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] , with nmrview and ccpnmr (http://www.ccpn.ac.uk/). programs for automated assignment of backbone and side chain signals are also available, such as pine and pine-sparky, which is included in the new version of sparky (nmrfam-sparky) , , mars , unio (assembly of match/ascan/candid/atnos algorithms) , , , , and flya , which is partially powered […]

PMCID: 4861749
PMID: 27023095
DOI: 10.1007/s10858-016-0029-x

[…] are accompanied by efficient visual verification tools: automated peak picking can be verified by a tool in nmrfam-sparky; errors in automated assignments by pine can be detected and corrected with pine-sparky (lee et al. ) or areca (dashti et al. ); and errors in automated structure calculations can be detected and corrected by the visual tools that are part of ponderosa analyzer., a goal […]


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PINE-SPARKY institution(s)
National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, USA

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