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CcpNmr specifications

Information


Unique identifier OMICS_34321
Name CcpNmr
Alternative name Collaborative Computational Project for NMR
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Basic
Version 3
Stability Beta
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Geerten Vuister

Publications for Collaborative Computational Project for NMR

CcpNmr citations

 (276)
library_books

Molecular mechanism of influenza A NS1 mediated TRIM25 recognition and inhibition

2018
Nat Commun
PMCID: 5940772
PMID: 29739942
DOI: 10.1038/s41467-018-04214-8

[…] 00 MHz. Samples were measured at concentrations ranging between 0.1 and 0.5 mM in 20 mM Na2HPO4, 150 mM NaCl, 0.5 mM TCEP at pH 6.5. All spectra were processed with NMRPipe and analysed using Sparky, CCPNMR and CARA (http://cara.nmr.ch). For backbone resonance assignments of the PRYSPRY domain, HNCACB, CBCA(CO)NH and HNCA spectra were recorded. Backbone resonance assignment was obtained to a compl […]

library_books

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2 25K

2018
Sci Rep
PMCID: 5934386
PMID: 29725124
DOI: 10.1038/s41598-018-25476-8

[…] . NMR spectra were processed using the NMRpipe program, and chemical shift assignments were accomplished using CARA. Analyses of relaxation and chemical shift perturbation experiments were done using CCPNMR. Secondary structures for wildtype, Q126L, D127G E2-25K were calculated from chemical shifts using the CSI 3.0 program. […]

library_books

Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB

2018
PMCID: 5890618
PMID: 29526435
DOI: 10.1016/j.str.2018.02.007

[…] ker AVANCE spectrometers operating at 500 MHz, 700 MHz and 950 MHz with TXI cryoprobes controlled by Topspin 3 (Bruker Biospin Ltd). Spectra were processed using NMRPipe/NMRDraw () and analyzed using CcpNMR Analysis 2.2 (). Backbone resonances were assigned in a standard manner using [1H,15N]-HSQC, HNCA, HNCACB, CBCA(CO)NH, and HNCO experiments (). Side-chains resonances assignment was performed u […]

library_books

The voltage gated sodium channel EF hands form an interaction with the III IV linker that is disturbed by disease causing mutations

2018
Sci Rep
PMCID: 5852250
PMID: 29540853
DOI: 10.1038/s41598-018-22713-y

[…] e titrated into a sample of 200 μM 15N-labelled EF-hand domain at final molar ratios of 0.25:1, 0.5:1, 1:1, 2:1, and 4:1. The data were processed with NMRPipe and analysed either with Sparky 3.114 or CcpNmr 2.4.2. The weighted amide 1HN-15N chemical shift perturbation were determined with the CcpNmr Follow Shift Changes tool using the standard settings, (Δδ = [(Δδ1H,ppm)2 + (0.15Δδ15N,ppm)2]1/2). […]

library_books

Phosphorylation of conserved phosphoinositide binding pocket regulates sorting nexin membrane targeting

2018
Nat Commun
PMCID: 5843628
PMID: 29520003
DOI: 10.1038/s41467-018-03370-1

[…] 13C, and 2H/15N/13C labeled protein were acquired at 298 K on 600 and 800 MHz Varian Inova spectrometers equipped with 5 mm cryogenic probes. The spectra were processed with NMRpipe and analysed with CCPNMR. The backbone 1H, 15N, and 13C resonances were sequentially assigned using standard 3D experiments. Distance restraints were derived from 15N-edited NOESY-HSQC and 13C-edited NOESY-HSQC experim […]

library_books

Disease Variants of FGFR3 Reveal Molecular Basis for the Recognition and Additional Roles for Cdc37 in Hsp90 Chaperone System

2018
PMCID: 5846801
PMID: 29478821
DOI: 10.1016/j.str.2018.01.016

[…] iments () and TROSY-detected HSQC experiments with water flip-back and WATERGATE pulses () were recorded as detailed previously. All data were processed using NMRPipe and NMRDraw () and analysed with CCPNMR Analysis (). […]

Citations

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CcpNmr institution(s)
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK ; Department of Biochemistry, University of Cambridge, Cambridge, UK
CcpNmr funding source(s)
Supported by MRC grant MR/L000555/1

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