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ncSPC specifications

Information


Unique identifier OMICS_26274
Name ncSPC
Alternative name Neighbor Corrected Structural Propensity Calculator
Interface Web user interface
Restrictions to use None
Input data Some NMR assignment data.
Input format TALOS
Computer skills Basic
Stability Stable
Maintained No

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Publication for Neighbor Corrected Structural Propensity Calculator

ncSPC citations

 (4)
library_books

Gcn4 Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein Protein Complex

2018
Cell Rep
PMCID: 5908246
PMID: 29562181
DOI: 10.1016/j.celrep.2018.02.097

[…] ted according to ΔδNH (ppm) = sqrt [ΔδH2 + (ΔδN/5)2]. Component 1H and 15N CSPs are (freeform—bound form) in ppm. Secondary structure propensity was determined from backbone chemical shifts using the Neighbor-Corrected Structural Propensity Calculator (ncSPC) (). Max CSP as in represents the maximum CSP of any residue within each defined hydrophobic cluster. […]

call_split

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP

2017
Sci Rep
PMCID: 5498717
PMID: 28680062
DOI: 10.1038/s41598-017-04611-x
call_split See protocol

[…] Secondary structure propensity analysis was calculated from C′, Cα, Cβ and N chemical shifts (95% assigned) by using the neighbor-corrected structural propensity calculator (ncSP) tool. For further details, cf. SI Materials and methods. […]

library_books

Transient helicity in intrinsically disordered Axin 1 studied by NMR spectroscopy and molecular dynamics simulations

2017
PLoS One
PMCID: 5371316
PMID: 28355271
DOI: 10.1371/journal.pone.0174337

[…] with z- and xyz-gradient cryoprobes, respectively. Spectra were processed with NMRPipe [] and analyzed with CcpNMR Analysis []. The secondary structure propensity (SSP) was derived by the online tool ncSPC [] (neighbour-corrected Structural Propensity Calculator), according to SSP=ΔδCα-ΔδCβ(3) where ΔδCα and ΔδCβ represent the difference between carbon α and carbon β Axin-1 experimentally obtained […]

library_books

Structural Plasticity in Human Heterochromatin Protein 1β

2013
PLoS One
PMCID: 3621757
PMID: 23585859
DOI: 10.1371/journal.pone.0060887

[…] –79) and CSD (107–176) and verified by additional standard TROSY-based 3D experiments when required.Secondary chemical shifts were calculated based on the random coil chemical shifts predicted by the Neighbor Corrected Structural Propensity Calculator and corrected for the 2H isotope shift. The 4,4-dimethyl-4-silapentane-1-sulfonic acid (0.0 ppm) was used for chemical shift referencing. Consensus […]

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ncSPC institution(s)
Biotransformation and Biocatalysis Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Aarhus, Denmark
ncSPC funding source(s)
Supported in part by a VIDI grant from the Netherlands Organization for Scientific Research (NWO).

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