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Protocols

PINE-SPARKY specifications

Information


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 citations

 (8)
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PINE SPARKY.2 for automated NMR based protein structure research

2017
Bioinformatics
PMCID: 5925765
PMID: 29281006
DOI: 10.1093/bioinformatics/btx785
call_split See protocol

[…] PINE-SPARKY.2 can be launched from the automated assignment sub-menu of NMRFAM menu or by typing the two-letter-code ep in the NMRFAM-SPARKY. This opens a graphical user interface that makes all the f […]

library_books

Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three dimensional Structure Determination of Proteins Open Avenues for Life Scientists

2017
Comput Struct Biotechnol J
PMCID: 5408130
PMID: 28487762
DOI: 10.1016/j.csbj.2017.04.001

[…] .org/en/nmr_tool_box/magro_nmrview.html) , 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 by the GARA […]

library_books

Integrative NMR for biomolecular research

2016
J Biomol NMR
PMCID: 4861749
PMID: 27023095
DOI: 10.1007/s10858-016-0029-x

[…] s 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 of Inte […]

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NMRFAM SDF: a protein structure determination framework

2015
J Biomol NMR
PMCID: 4569665
PMID: 25900069
DOI: 10.1007/s10858-015-9933-8
call_split See protocol

[…] iated with particular NMR experiments.Fig. 4ADAPT-NMR Enhancer and ARECA can be used to validate the chemical shift assignments generated by ADAPT-NMR. Validation of PINE’s output can be performed by PINE-SPARKY (Lee et al. ) (incorporated into NMRFAM-SPARKY), or the ARECA package. […]

library_books

NMR Studies of the Dynamics of High Spin Nitrophorins: Comparative Studies of NP4 and NP2 at Close to Physiological pH

2014
Biochemistry
PMCID: 4303294
PMID: 25486224
DOI: 10.1021/bi501305a

[…] ases, the temperature was maintained at 30 °C. 2D 1H{15N} HSQC, 3D HNCA, 3D HN(CA)CO, 3D HNCO, 3D HNCACB, and 3D CBCA(CO)NH peak lists for NP4 were used as input to the PINE server and, employing the PINE-SPARKY extension, were used to determine sequence-specific backbone resonance assignments. Assignment data were collected at pH 7.3 for NP4, referenced to DSS, and are listed in Table S1 of the . […]

library_books

Solution Structure of the 2A Protease from a Common Cold Agent, Human Rhinovirus C2, Strain W12

2014
PLoS One
PMCID: 4061012
PMID: 24937088
DOI: 10.1371/journal.pone.0097198

[…] e, by stepwise judicious selection of cloning vector (pE-SUMO), host strain, isolation and purification protocols, the C105A mutation, and solution conditions. Linkage of the output from PINE-NMR to PINE-SPARKY validations facilitated and virtually automated the spectral peak assignments. The final structure was of high quality and well supported by the extensive datasets. […]


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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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