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CheShift specifications

Information


Unique identifier OMICS_05519
Name CheShift
Alternative name CheShift-2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainer


  • person_outline CheShift Team

Additional information


https://pymolwiki.org/index.php/Cheshift

Information


Unique identifier OMICS_05519
Name CheShift
Alternative name CheShift-2
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
License MIT License
Computer skills Medium
Version 3.6
Stability Stable
Requirements
PyMOL
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline CheShift Team

Additional information


https://pymolwiki.org/index.php/Cheshift

Publications for CheShift

CheShift citations

 (3)
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

[…] ded to sample the standard deviation in the chemical shift energy term. The ClusCo program was used to extract a representative 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 perform […]

library_books

ProCS15: a DFT based chemical shift predictor for backbone and Cβ atoms in proteins

2015
PeerJ
PMCID: 4662583
PMID: 26623185
DOI: 10.7717/peerj.1344

[…] tively, 2.2 (2.8) ppm, 0.7 (0.6) ppm, and 4.7 (4.6) ppm for ProCS15 (PCM/OPBE/6-31G(d,p)). These accuracies are very similar to DFT-based predictions made by other researchers (e.g., ; ; ) as well as CheShift-2 (), which is another DFT-based chemical shift predictor for Cα and Cβ atoms. The RMSD values computed using ProCS15 for Ubiquitin can be reduced by as much as 0.7, 0.1, and 0.5 ppm for carb […]

library_books

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

2013
PLoS One
PMCID: 3877219
PMID: 24391900
DOI: 10.1371/journal.pone.0084123

[…] chemical shifts.We are currently working on implementing a QM-based chemical shift prediction method for the remaining H, C, and N nuclei in a protein in ProCS (unfortunately, the source code of the CheShift method developed by Vila et al. for QM-based C chemical shift prediction is not available). The resulting ProCS/PHAISTOS interface should provide a powerful tool for chemical shift-based prot […]

Citations

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CheShift institution(s)
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA; Universidad Nacional de San Luis, IMASL-CONICET, San Luis, Argentina; Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; Institute of Bioinformatics and Structural Biology, Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan; California Institute of Quantitative Biosciences (QB3) and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
CheShift funding source(s)
Supported by grants GM71862 (HJD), DP5OD009180 (JSF), GM14312 (HAS) from the National Institutes of Health and PIP-112–2011–0100030 (JAV) from IMASL-CONICET, Argentina.

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