PINE-NMR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PINE-NMR

Tool usage distribution map

This map represents all the scientific publications referring to PINE-NMR per scientific context
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PINE-NMR specifications


Unique identifier OMICS_06815
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PINE-NMR

PINE-NMR citations


Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release

Nat Commun
PMCID: 5738438
PMID: 29263320
DOI: 10.1038/s41467-017-02308-3

[…] ple resonance experiments was carried out on the 13C, 15N-labeled Npm tail domain (HNCA, HNCACB, HNCO, HN(CO)CA, CBCA(CO)NH, HN(CA)CO, and HBHA(CO)NH). Resonances were assigned using a combination of PINE NMR server predictions and manual inspection of the spectra. CSPs upon NaCl and histone titration were calculated using the following equation:1CSP=(ΔδHN)2+(ΔδN*αN)2,Where ΔδHN is the change in c […]


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

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

[…] re solved here, 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. […]


ADAPT NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy

PMCID: 3570218
PMID: 23220573
DOI: 10.1093/bioinformatics/bts692

[…] ular tilted plane that will identify peaks in the 3D spectrum. ADAPT-NMR incorporates an earlier approach to fast data collection, HiFi-NMR () and an algorithm for automated probabilistic assignment, PINE-NMR (). The output from ADAPT-NMR is a probabilistic assignment table and analysis of secondary structure. As a means for visualizing the spectral data, picked peaks and spin system assemblies un […]


PONDEROSA, an automated 3D NOESY peak picking program, enables automated protein structure determination

PMCID: 3106192
PMID: 21511715
DOI: 10.1093/bioinformatics/btr200

[…] (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) software package described here bridges this gap and is meant to be used with an automated resonance assignment package such as PINE-NMR introduced earlier by our group (). […]


The Center for Eukaryotic Structural Genomics

J Struct Funct Genomics
PMCID: 2705709
PMID: 19130299
DOI: 10.1007/s10969-008-9057-4
call_split See protocol

[…] ational ANalysis) then carries out probabilistic secondary structure determination.The separate data analysis steps (PISTACHIO, LACS, and PECAN) have now been fully integrated into a pipeline, called PINE-NMR. PINE handles input data from a wide variety of NMR experiments, including HCCH TOCSY (important for side chain assignments). PINE is freely available from a web server (http://miranda.nmrfam […]

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

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