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CamShift specifications

Information


Unique identifier OMICS_05516
Name CamShift
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

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Publication for CamShift

CamShift citations

 (11)
library_books

The PROSECCO server for chemical shift predictions in ordered and disordered proteins

2017
J Biomol NMR
PMCID: 5711976
PMID: 29119515
DOI: 10.1007/s10858-017-0145-2

[…] uate secondary structure elements from protein chemical shifts. Additional entries to the parameterizing dataset were employed exclusively for benchmarking PROSECCOFOLDED, SPARTA+ (Shen and Bax ) and CamShift (Kohlhoff et al. ). In particular, the selected benchmark database contained 77 BMRB entries having all been deposited after 2016, which ensured that these data were not part of the parameter […]

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

[…] ple, molecular size or chemical exchange processes . As an alternative approach, dihedral angles and the secondary structure of proteins are predicted by the programs TALOS (and related versions) , , CamShift and SHIFTX2 . These programs use prior chemical shifts statistics, including 1HN, 15N, 13Cα, 13Cβ, 1Hα and carbonyl 13C nuclei, with corresponding structure coordinates.Dihedral angle inform […]

library_books

Emergence and evolution of an interaction between intrinsically disordered proteins

2017
eLife
PMCID: 5419745
PMID: 28398197
DOI: 10.7554/eLife.16059.028

[…] etainference (, ). Prior information contained in the Charmm22* force field () with explicit solvent. Chemical shifts (Cα, Cβ, N and H) were included using Metainference in its Gaussian form () using CamShift (; ) over N = 10 replicas, r. The Metainference energy was calculated as:E=∑r=1N{Eff+kBT∑i=1Nd[(fi(X)−di)22σr,i2+0.5log2πσr,i+0.5logσr,i]}where the first term is the sum the over the replicas […]

call_split

Protein structure refinement using a quantum mechanics based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

2016
PMCID: 5399634
PMID: 28451325
DOI: 10.1039/c6sc04344e
call_split See protocol

[…] e structure from the ensemble using hierarchical agglomerative clustering.CheShift-2 () calculations were performed with the CheShift-2 PyMOL-plugin found at ; http://github.com/aloctavodia/cheshift. CamShift, PPM One, Sparta+, shAIC, and ShiftX2 () calculations are performed using the stand-alone predictors. Scripts to automate these predictions can be found at ; http://github.com/larsbratholm/cs […]

library_books

Interaction Networks in Protein Folding via Atomic Resolution Experiments and Long Time Scale Molecular Dynamics Simulations

2015
J Am Chem Soc
PMCID: 4648500
PMID: 25924808
DOI: 10.1021/jacs.5b02324

[…] ranging from 0.5 to 50 μs., In order to obtain consistent clustering, this analysis was simultaneously performed on the five trajectories combined. Chemical shift predictions were performed using the CamShift and SPARTA+ programs. Helical residues for the analysis of the autocorrelation function were identified according to the STRIDE definition, as implemented in VMD. […]

library_books

Bayesian inference of protein structure from chemical shift data

2015
PeerJ
PMCID: 4375973
PMID: 25825683
DOI: 10.7717/peerj.861

[…] ical force field.Simulations were performed on three small proteins (ENHD, Protein G and SMN Tudor Domain) for a Gaussian and Cauchy-based probability distribution, using the chemical shift predictor CamShift (). The ISD-determined uncertainties were found to correspond well to the empirically determined uncertainties in the CamShift predictions. Furthermore sampling the uncertainties as part of t […]

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CamShift institution(s)
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK

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